Methods of novel therapeutic candidate identification through gene expression analysis in vascular-related diseases

ABSTRACT

The present invention discloses multiple treatment regimens for vascular-related diseases and disorders. The present invention provides for methods of treating vascular-related disorders based on gene expression studies from samples collected from individuals having symptoms of vascular-related disorders. Additionally, methods are disclosed involving diagnostic techniques to focus treatment regimens. Finally, methods of treating vascular-related disorder involving targeting microRNAs are also disclosed.

CROSS-REFERENCES

This application claims the benefit of priority of U.S. ProvisionalApplication Ser. No. 61/040,065, filed on Mar. 27, 2008, the disclosureof which is hereby incorporated by referenced in its entirety.

FIELD OF THE INVENTION

The present invention relates to assessment and identification ofexpression of genes related to vascular-related diseases. The presentinvention also includes methods of comparing gene expression patternswith respect to various disease states.

BACKGROUND OF THE INVENTION

Pulmonary arterial hypertension (PAH) is an occlusive disease of thepulmonary arteries leading to serious hemodynamic abnormality, rightheart failure, and premature death. The molecular mechanisms behind PAHare still unclear. Without a more complete understanding of PAH and howits complex vascular dysfunctions relate to one another, patients willsuffer from imprecise diagnosis and drug therapy that may be less thanoptimal. Despite recent advances and introduction of new clinicallyapproved drugs, the 5-year survival from pulmonary hypertension remainsan estimated 50% (Archer and Rich, 2000). Consequently, treatment forPAH, while recently improved, still offers significant and long-lastingimprovement in only a minority of patients. A methodology to elucidatethe molecular pathways associated with PAH could guide the developmentof new therapies for this disease.

Though platelets and other cells may have a role in PAH, pulmonaryendothelial cells and pulmonary smooth muscle cells appear to be theprimary sites of disease progression (Humbert et al 2004). Molecularpathways that show abnormality in pulmonary endothelial cells andpulmonary smooth muscle cells during PAH include endothelin-1 (Giaid etal 1993), serotonin & serotonin transporter (Marcos et al 2003),thromboxane (Walmrath et al 1997), nitric oxide synthase (Kobs andChesler 2006), prostacyclins (Gailes, et al 2001), potassium channels(Mandegar et al 2002), BMP signaling (Eddahibi et al 2002), and survivin(McMurtry et al 2005). PAH impairs normal signaling and growth in bothpulmonary endothelial and pulmonary smooth muscle cells, yet thecellular abnormalities seem to shift over time in unpredictable patternsthat has thus far escaped concise definition (Michelakis, 2006).

PAH may be understood as proceeding in phases. In early PAH, endothelialapoptosis occurs, probably resulting in pulmonary arteriole plugging andan increase in pulmonary vascular pressure (Michelakis, 2006). In latePAH, chronic exposure to elevated pulmonary artery pressure togetherwith dysfunctional endothelial signaling initiates hyperproliferation ofsmooth muscle cells (McMurtry et al 2005). Increased concentricpulmonary smooth muscle cell proliferation leads to ever increasingpulmonary artery pressure, right ventricular failure, and death.

Lung pathology in all PAH patients show thickening throughout thearterial wall of the pulmonary vascular bed. In some forms of thedisease, the pulmonary vascular lesions are reversible (e.g. in newbornswith congenital heart defects). In other patients, such as those withthe idiopathic form, the lesions are irreversible. It is unknown howthese variations in PAH relate to one another on a molecular basis(Pearl et al 2002).

Current therapies for PAH patients primarily target vascular tone.Treatments that aim at correcting potassium channel dysfunction (Machadoet al 2001), nitric oxide impairment (Humbert et al 2004), prostacyclinimpairment (Tuder et al 1999, Christman et al 1992), and endothelin-1expression (Giaid et al 1993) have all been clinically available forseveral years. These therapies offer some relief from hemodynamicsymptoms, but most patients show only a transient response. Theproliferative disease continues to progress in most PAH patients,resulting in a five year mortality rate that remains at around 50%(Newman et al 2004).

Currently, there are no clinically available routine means to obtainendothelial and smooth muscle samples from the pulmonary arteries ofpulmonary hypertension patients for diagnosis, disease staging or drugdiscovery. Applicant's earlier invention, described in U.S. Pat. No.5,406,959, describes an endoarterial biopsy catheter that hasdemonstrated its safety and effectiveness in normal canines (Rothman,Mann et al., 1996), canines with experimentally-induced pulmonaryhypertension (Rothman, Mann et al., 1998), and canines with single-sidedlung transplant rejection (Rothman, Mann et al., 2003). Preliminarystudies have also demonstrated the safety and efficacy of acatheter-based method to obtain endovascular samples from a porcinemodel of PAH.

Percutaneously-obtained pulmonary endoarterial biopsy samples were foundto be of sufficient quantity and quality for porcine whole genome mRNAmicroarray analysis and microRNA analysis. Whole genome microarrayanalysis revealed time-sensitive variations in gene expression values asPAH progressed in the subject animal model. Genes previously shown to beassociated with PAH displayed changes characteristic of the disease, andgenes previously unassociated with PAH also displayed expression leveldysregulation. These findings raise the possibility that theendoarterial biopsy catheter combined with microarray analysis mayprovide a valuable platform for the discovery of novel drug andbiomarker targets in pulmonary hypertension and a platform to deliverindividualized pharmacotranscriptomics.

MicroRNA analysis revealed pressure sensitive changes in microRNAexpression. As our surgical shunt model of pulmonary hypertensionprogressed from a high flow low pressure (HFLP) manifestation to a highflow high pressure (HFHP) manifestation, different microRNAs becamedysregulated either increasing or decreasing in expression relative toour baseline normal values.

Most new therapies promise to focus on arresting either the endothelialapoptosis that characterizes early PAH (angiopoetin-1 & endothelialnitric oxide synthase cell-base gene transfer (Zhao et al 2003; 2005),caspase inhibitors (Taraseviciene-Stewart at al 2001)) or the smoothmuscle cell proliferation typical of late PAH (dichloroacetate (McMurtryet al 2004), simvastatin (Nishimura et al 2003), sidenafil (Wharton etal 2005), imatinib (Schermuly et al 2005), anti-survivin (McMurtry et al2005), K+ channel replacement gene therapy (Pozeg et al 2003)).

Before administering therapies, however, it would be extremely valuableto determine which genes are dysregulated in each PAH patient at anystage of their individual disease progression. Without knowing whatgenes are aberrant during any point in the patient's disease course,targeted therapies may miss the mark in some patients. Life threateningside effects may emerge if the wrong cells, at the wrong time, areencouraged to die or proliferate in patients with compromised pulmonaryvascular health.

A powerful method for determining the gene expression levels ofthousands of genes simultaneously are DNA microarrays. Initially usedfor the classification of cancers that were difficult to discriminatehistologically (Golub et al 1999, Bhattacharjee et al 2001, andRamaswamy et al 2001), microarrays have been more recently applied toPAH (Geraci et al 2001). PAH microarray studies have been performed onwhole lung homogenates in humans (Fantozzi et al 2005) and rats(Hoshikawa et al 2003), surgically-dissected pulmonary arteries in pigs(Medhora et al 2002), laser-microdissected pulmonary arteries in rats(Kwapiszewska et al 2005), and mononuclear peripheral blood in humans(Bull et al 2004). These studies have been performed to discoverpotentially novel PAH disease pathways, biomarkers, therapeutic targetsand patient classification gene expression profiles.

To advance PAH microarray studies into practical clinical use, tissueprocurement methodologies are required that do not require surgicalexplant or postmortem procurement, and peripheral blood has thus farproven to be inadequate to discriminate gene expression signaturesbetween subgroups of PAH patients (Bull et al 2004; Bull et al 2007). Totake advantage of the full power of microarray technologies in PAHpatients, a safe and effective minimally invasive means for the repeatprocurement of endovascular samples from living PAH patients isrequired.

The present invention provides for the use of a novel interventionalcatheter, an endoarterial biopsy catheter, to obtain serial biopsyspecimens from hypertensive pulmonary vessels for analysis. The abilityto procure endothelial and smooth muscle samples in a minimally invasivemanner will allow physicians to use microarray profiling and othertechniques to classify patients upon initial presentation according totheir gene expression signatures, prescribe therapies that target genesempirically found to be dysregulated in each individual patient, andmonitor and adjust PAH patient therapy according to subsequent biopsyfindings. A greater understanding of the complex molecular pathwaysunderlying each patient's PAH should enable more precise diagnosis andthe delivery of more effective therapies. Also of importance is theability to discover new uses for existing drugs as well as discoveringnew drug targets.

Individualized pharmacotranscriptomics based on endoarterial biopsy andmicroarray analysis represents a reasonable choice for researchersstruggling with the complexities and contradictions of PAH and othervascular diseases. The huge literature generated from in vitro andanimal studies falls short, at times, in addressing the actual facts ofpatient health. Many commentators describe this dilemma as the“bench-to-bedside gap”, where in vitro and animal laboratory data failsto model human disease circumstances (Aird, 2004). Bridging that gapthrough catheter-based access to the vasculature in a model thatrecapitulates the clinical and histopathological manifestations of aform of human pulmonary hypertension will likely enable closercorrelations between animal studies and patient care, and serve as amodel for other vascular-based diseases such as atherosclerosis,congestive heart failure, sickle cell disease, organ transplantrejection, connective tissue diseases, chronic obstructive pulmonarydisease, pulmonary embolism, asthma, systemic inflammatory response,battlefield trauma, cancer, sepsis and acute respiratory distresssyndrome. There is a need in the art to provide data from geneexpression analyses in order to target novel candidates for use intreating or preventing PAH.

SUMMARY OF THE INVENTION

One aspect of the present invention provides for methods of treating anindividual suffering from a vascular-related disease comprising thesteps of:

a) obtaining a biopsy sample from the individual's pulmonary artery;

b) analyzing gene expression levels of the biopsy sample from thepulmonary artery of the individual and a non-diseased control;

c) comparing the gene expression levels between the biopsy sample fromthe pulmonary artery of the individual and the non-diseased control;

d) identifying at least one gene from step c) that is upregulated ordownregulated in the biopsy sample based on the non-diseased control;

e) obtaining gene products from the genes identified in step c); and

f) selecting pharmaceutical agents which are known inhibitors of thegene products from the at least one upregulated gene or known promotersof the gene products from the at least one downregulated gene. Anadditional aspect to the present invention provides for thepharmaceutical agents selected for administration to the individualsuffering from the vascular-related disease. In yet another aspect, theindividual is categorized based on progression of the vascular-relateddisease, with the treatment being based on the timing of the disease.

Another aspect of the present invention provides for a means ofcomparing varying levels of gene expression based on an animal model forpulmonary arterial hypertension. In a preferred embodiment, the genesexpressed in the animal model are genes found to be either upregulatedor downregulated. In a more preferred embodiment, the upregulated ordownregulated genes are time-dependent based on the time after exposureto the PAH.

Another aspect of the present invention provides for methods ofidentifying genes involved in the pathway of PAH based on differentialgene expression studies in a time-dependent animal model for PAH. In oneembodiment, the genes are compared to other known genes which areupregulated or downregulated in the known PAH pathway.

Yet another aspect of the present invention provides for methods ofdiagnosing a vascular-related disease in an individual comprising thesteps of:

a) identifying at least one gene that is upregulated or downregulated inthe vascular-related disease comprising the steps of:

-   -   1) obtaining a biopsy sample from the individual's pulmonary        artery during progression of the vascular-related disease;    -   2) obtaining a pulmonary artery sample from a non-diseased        control;    -   3) extracting RNA from the samples in steps 1) and 2);    -   4) obtaining gene products from the RNA extracted in step 3);        and    -   5) comparing gene expression levels from the biopsy sample with        the non-diseased control, and

b) associating the genes upregulated in the biopsy sample with aninhibitor of the gene products for administration to the individual andgenes downregulated in the biopsy sample with a promoter of the geneproducts for administration to the individual.

Another aspect of the present invention provides for methods of treatingan individual having a vascular-related disease by targeting microRNAscomprising the following steps:

a) assessing a stage of the vascular-related disease in the individual;

b) identifying whether microRNAs are upregulated or downregulated;

c) selecting the microRNAs to target based on the stage of thevascular-related disease and whether the microRNAs are upregulated ordownregulated; and

d) administering an agent known to inhibit an upregulated microRNA or anagent known to promote a downregulated microRNA to the individual. Avariation of this embodiment provides for the stage of thevascular-related disease being based on flow rates and blood pressurewithin an artery of the individual.

Another aspect of the present invention provides for methods oftherapeutically targeting microRNA dysregulated in PAH comprising thesteps of:

-   -   (a) obtaining a biopsy sample from the pulmonary artery during        the progression of PAN;    -   (b) obtaining a pulmonary artery sample from a non-diseased        control;    -   (c) extracting RNA from the artery samples;    -   (d) converting the RNA to cDNA;    -   (e) comparing levels of microRNA expression at the two differing        times;    -   (f) identifying microRNA dysregulated in PAH relative to        baseline; and    -   (g) inhibiting upregulated microRNA or promoting downregulated        microRNA identified in PAH biopsies.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a surgical shunt model of PAH and its association withcongenital heart disease (CHD).

FIG. 2 depicts the endoarterial biopsy procedural configuration.

FIG. 3 depicts biopsies: normal vessels at baseline, hypertensive LPA at7, 21, 60 and 180 days post shunt.

FIG. 4 depicts GeneSpring downstream analysis of microarray data.

DETAILED DESCRIPTION OF THE INVENTION

The model described in the present invention is surgically-induced PAHin pigs. Our model mimics human Eisenmenger syndrome (a form of PAHrelated to congenital heart malformation) in both symptoms and pathology(Corno et al 2003). The size of the animals makes the pulmonary vesselsavailable to the catheter, providing a ready transition to humanclinical use. And finally, the commercial availability of whole genomeporcine microarrays (Bai et al 2003) makes the species ideal for ourpurposes in the study, and renders the use of cross species microarraysunnecessary (Medhora et al 2002).

By obtaining pulmonary endovascular samples at early, intermediate andlate time points in PAH progression, and analyzing these samples usingporcine whole genome microarrays, a time-sensitive microarray based mapof the underlying molecular biology of PAH may be obtained. Improvedknowledge of the molecular mechanisms underlying PAH progression canlead to the identification of stage-specific biomarkers, new therapeutictargets for drug intervention, and novel signaling pathways involved inthe pathogenesis of PAH. These novel target genes can then be validatedusing quantitative PCR and immunohistochemical stains on porcineendoarterial biopsy samples procured concurrently. At the same time, thecombination of minimally invasive endoarterial biopsy and whole genomemicroarray analysis can serve as an animal model for subsequent studiesin PAH patients.

The following examples provided in this disclosure provide a profilegene expression in pulmonary hypertensive pigs by surgical anastomosisof the left pulmonary artery to the descending aorta. Endoarterialbiopsy samples are collected from animals with a surgical shunt model ofpulmonary hypertension at multiple time points over a 6-month timecourse. Gene expression analysis of the biopsy samples was performed onporcine microarrays. Microarray analysis was performed to detectdysregulated genes previously unassociated with PAH, discover novelbiomarkers of pulmonary hypertension and novel targets for therapeuticintervention and advance knowledge of the molecular mechanisms ofpulmonary hypertension. These studies will also help validate a newplatform for PAH diagnosis and drug discovery, endoarterial biopsy andmicroarray analysis, for eventual clinical practice.

EXAMPLES Example I Construction of a Microarray-Based Map of Changes inGene Expression During the Progression of PAH and the Identification ofNovel Therapeutic Candidates

In an animal model of PAH created by Antonio Corno and colleagues, pigsundergo surgery that redirects systemic circulation into the leftpulmonary artery mimicking pulmonary hypertension secondary tocongenital heart disease. The surgery elevates PA pressure and createsthe same hemodynamic conditions that PAH patients experience. Thepresent study investigates how the elevated pressure remodels thepulmonary vasculature. In Corno's studies, histology on necropsyconfirmed intimal hyperplasia in the pulmonary arteries, evidence thatthe surgical shunt surgery described will cause endovascular remodeling(Corno et al 2003).

Biopsy Extraction and Surgery Protocol

20-30 kg Yucatan Micropigs (Sus scrofa, Yucatan micro breed) underwentsurgical anastomosis of the left pulmonary artery to the descendingaorta, resulting in left pulmonary arterial hypertension of at least ½systemic levels. Animals are penned in the laboratory for no less thanone week prior to surgery and fed normal chow. On surgery day, animalswere premedicated with 20 mg/kg intramuscular ketamine and 0.1 mg/kgintramuscular midazolam. After 0.25 mg of intramuscular atropine,anesthesia was induced with 1 mg/kg intravenous midazolam and 0.1 mg/kgintravenous fentanyl and maintained with 0.1 mg/kg/hr intravenouspancuronium bromide. Pigs were ventilated with an inspired oxygenfraction (FiO2) of 0.4, a tidal volume of 15 ml/kg, and a respiratoryrate of 12 breaths/minute. One gram of intravenous cefazolin was givenbefore and 2 hours after the surgical procedure. Surgical and catheterprocedures were performed under general anesthesia with endo-trachealintubation. Sedation medications and anesthetics were administered by ananesthesiologist. Intra-cardiac and intravascular pressures, EKG, andblood oxygen saturations were monitored continuously.

Under sterile conditions (the thoracic area was shaved and prepared withbetadine, a left thoracotomy was performed through the fourthintercostal space, about 5 centimeters, to expose the great arteries.The main pulmonary artery (MPA) and its branches were identified andfreed from surrounding tissue. Two clamps were placed on the proximalleft pulmonary artery (LPA). The proximal LPA was sutured closed, usingprolene, and the distal LPA was sutured end to side in a clamped regionin the descending aorta (FIG. 1), using cardiovascular prolene. Piecesof LPA endoarterial tissue were taken for histology. The clamps wereremoved and an IV dose of 1 mg/kg Furosemide immediately given.Hemostasis was obtained with sutures and cautery. Direct needle bloodpressures were recorded in the main pulmonary artery and in the newlyanastomosed left pulmonary artery. The chest was closed with sutures,both subcutaneous and cutaneous layers, using prolene and surgical wire.The animals then were weaned from anesthesia and mechanical ventilation.Postoperative analgesia was provided with morphine four times a day anda 1-2 mg/kg dose from 0.25% solution of IV Bupivacaine, a localanesthetic. A circulating warming blanket was used during surgery andrecovery.

Endoarterial biopsies were performed at baseline prior to surgery toobtain unaffected tissue, and at post-shunt timepoints to obtainhypertensive biopsy samples (FIG. 2). Follow up endoarterial biopsyprocedures were scheduled 7, 21, 60 and 180 days after surgery. On eachcatheterization day, animals were premedicated with 10 mg/kg of IVpropofol, were intubated and ventilated at a rate of 12 breaths/min andwere maintained under anesthesia with 1.5% halpthane. A femoral arteryline was placed for monitoring. To obtain biopsies from the hypertensiveleft lung, an 8F introducer is placed in a carotid artery, and a 7Fendhole catheter is advanced into the aorta. An angiogram is performedto visualize the LPA-aortic anastomosis. The 7F endhole catheter is thenthreaded through the anastomosis with X-ray fluroscopic guidance. Anangiogram of the hypertensive left pulmonary vascular tree is thenperformed, and the catheter is advanced to the distal pulmonary arteryselected for biopsy. A 0.038 in, 260 cm extra stiff Amplatz exchangeguide wire will then be passed through the end-hole catheter. Theend-hole catheter was exchanged for a long flexible 8F introducer sheaththat is adapted with a radio opaque band at the distal end and shaped toconform to the vascular pathway. A 7F angiographic catheter was advancedthrough the sheath in to a 2.5 mm to 3.0 mm distal pulmonary arterybranch, where an angiogram was obtained. The angiographic catheter willserve as a guide to advance the stiff sheath into a small vesseltargeted for biopsy and will then be exchanged for the endoarterialbiopsy catheter.

The endoarterial biopsy catheter has an external diameter of 2.5 mm andis composed of two flexible polymeric tubes that slide relative to eachother. The inner tube has a stainless steel distal end with a beveledopening that is designed to accommodate arterial tissue. A vacuum iscoupled to the inner tube and channeled to the beveled opening. Theouter tube terminates in a stainless steel cutting tube. The proximalends of the two tubes are with a spring powered operating mechanism. Toobtain the biopsy sample a vacuum is transmitted to the beveled openingof the inner tube, causing a tissue sample to be drawn in. The outertube is then advanced over the inner tube, severing the tissue sample.With this design, the area of artery contacted by the outer periphery ofthe beveled opening is larger than the inner aperture connected to thevacuum, this maintaining the tissue sample with its orientationpreserved. After each biopsy, the catheter was removed and the tissuesample was placed in the appropriate solution for further processing andanalysis. After the biopsy procedures were completed, repeatedangiograms were obtained to assess the degree of vascular injury. At theend of the procedure, the biopsy catheter and introducer sheath wereremoved and hemostasis was obtained by surgical repair of the carotidartery. The animals will then be weaned from anesthesia and mechanicalventilation. Postoperative analgesia was provided with morphine fourtimes a day and or fentanyl patches and non-steroidal anti-inflammatorydrugs four times a day.

Tissue Processing

For microarray analysis, biopsy samples are placed in a test tubecontaining RNAlater (Qiagen), flash frozen in dry ice, and kept frozenuntil RNA extraction. Additional samples are preserved in formalin, OCTfreezing solution, or Bouin's solution for subsequentimmunohistochemical and quantitative PCR analysis.

Porcine Genome Arrays

The Affymetrix GeneChip® Porcine Genome Array provides comprehensivecoverage of the Sus scrofa transcriptome. The array contains 23,937probe sets that interrogate approximately 23,256 transcripts from 20,201Sus scrofa genes.

The sequence information for this array was selected from public datasources including UniGene Build 28 (August 2004), GenBane mRNAs up toAug. 24, 2004, and GenBank® porcine mitochondrial and rRNA sequences.Probe sets consist of up to eleven probe pairs. The array formatconsists of eleven micron features synthesized on the 100 format.

RNA Extraction from Endoarterial Biopsy Samples

RNA was prepared from fresh frozen endoarterial biopsy samples in asegregated laboratory, specially prepared and cleaned regularly todestroy nucleases. Specimens were homogenized using QIAshredder columns(Qiagen, Valencia, Calif.) utilized in a FastPrep FP120 Homogenizer(Thermo Electron Corporation, Waltham, Mass.). RNA was isolated usingRNeasy Mini columns (Qiagen, Valencia, Calif.) as per manufacturer'sprotocol. All total RNA was eluted in nuclease free water, and quantitywas established by UV spectrophotometer. Final RNA integrity wasevaluated by capillary electrophoresis on the Agilent 2100 Bioanalyzer(Agilent, Palo Alto, Calif.).

Gene Expression

Before target production, the quality and quantity of each RNA samplewas assessed using a 2100 BioAnalyzer (Agilent). Target was prepared andhybridized according to the “Affymetrix Technical Manual”. Total RNA(ug) was converted into cDNA using Reverse Transcriptase (Invitrogen)and a modified oligo (dT)24 primer that contains T7 promoter sequences(GenSet). After first strand synthesis, residual RNA was degraded by theaddition of RNaseH and a double-stranded cDNA molecule was generatedusing DNA Polymerase I and DNA Ligase. The cDNA will then be purifiedand concentrated using a phenol:chloroform extraction followed byethanol precipitation. The cDNA products will then be incubated with T7RNA Polymerase and biotinylated ribonucleotides using an In VitroTranscription kit (Enzo Diagnostics). One-half of the cRNA product waspurified using an RNeasy column (Qiagen) and quantified with aspectrophotometer. The cRNA target (20 ug) was incubated at 94° C. for35 minutes in fragmentation buffer (Tris, MgOAc, KOAc). The fragmentedcRNA was diluted in hybridization buffer (MES, NaCl, EDTA, Tween 20,Herring Sperm DNA, Acetylated BSA) containing biotin-labeled OligoB2 andEukaryotic Hybridization Controls (Affymetrix). The hybridizationcocktail was denatured at 99° C. for 5 minutes, incubated at 45° C. for5 minutes and then injected into a GeneChip® cartridge. The GeneChip®array was incubated at 42° C. for at least 16 hours in a rotating ovenat 60 rpm, GeneChips® were washed with a series of nonstringent (25° C.)and stringent (50° C.) solutions containing variable amounts of MES,Tween20 and SSPE. The microarrays will then be stained with StreptavidinPhycoerythrin and the fluorescent signal was amplified using abiotinylated antibody solution. Fluorescent images were detected in aGeneChip® Scanner 3000 and expression data was extracted using theGeneChip® Operating System v 1.1 (Affymetrix). All GeneChips® werescaled to a median intensity setting of 500. Gene expression levels werecompared between biopsy samples taken from the control distal pulmonaryvasculature (baseline LPA and RPA) and PAH distal pulmonary arteries(surgical shunt LPA).

Gene Expression Analysis

After RNA preparation, array hybridization and scanning of the PorcineGeneChips® exactly as recommended by Affymetrix, the data produced areprocessed using the Affymetrix tools in the R-Eioconductor packagecalled /Affy/. This tool set allows for various probe level analyses ofthe data as well as probe level quality control. The MASS algorithm wasused, taking into account both the MM and PM probe data, and generating“Present” or “Absent” calls for each gene on each chip. If boxplots ofthe porcine probe level data reveal that any of the hybridizations areof low quality, the data from these chips was removed from anydownstream analysis. MASS with the non-linear Quantiles normalization(Affy package/normalize.quantiles)/ was used with this data set toproduce data almost free of artificial correlations. The Present/Absentcalls are also used to remove from the analysis the genes that werenever expressed in any of the samples examined (this is analogous tousing a P-value for gauging a gene's data quality on a chip, and thenfiltering).

Based on the first dozen chips processed, after normalization andquality control ˜19,000 genes were moved on to the next stage of theanalysis. The commercial package GeneSpring was used to assessdifferential gene expression and perform tests using clusteringalgorithms. Thus far, hierarchical clustering has revealed that thetime-point replicates have the greatest similarity to one another.

Gene expression fold changes for 7, 21 60 and 180 days post-surgeryrelative to baseline were then loaded into GSEA (gene set enrichmentanalysis) or specially written PERL scripts which carry out KS(Kolmogorov-Smirnov) statistical analysis in order to identify noveltherapeutic candidates.

Novel Therapeutic Identification

During PAH the best therapeutic targets are those which are upregulatedas the disease state progresses. Thus drugs which are known to counterthe action of any upregulated genes and their products would be of thegreatest potential therapeutic value. Therefore, lists of upregulatedgenes were then matched to drugs which target their gene products.

In addition, many drugs interact with multiple targets in the body'stissues. Lists of the targets (called genesets) for each of ˜2000characterized drugs were obtained from the literature and onlinedatabases. These genesets were then used to search for drugs which wouldbe most likely to have therapeutic value in PAH.

This was done by using KS statistics which computes theKolmogorov-Smirnov score for a geneset for a particular drug within anordered list. The KSscore task is used to examine the enrichment of aset of genes at the top of an ordered list. The KS score is high whenthe tags appear early (i.e. near the top) of the ordered list. Thesignificance of the KS score for a particular test may be examined bycomputing KS scores for multiple sets of X query genes selected atrandom from the dataset (note that the KS score is not independent ofthe number of members of the query gene set). Using this approach wewere able to identify in our messenger RNA expression dataset drugswhich are currently used as therapeutics for PAH (see FIG. 1A).Importantly, using the same approach we were also able to identifyadditional potential therapeutics, within the existing pool ofcharacterized drugs. This process identified existing drugs as noveltherapeutics for PAH.

Example II Gene Expression Analysis from Porcine Animal Model Data

Gene Expression Analysis

The porcine studies indicate that single endoarterial biopsy samplesobtained in the porcine model of surgical shunt PAH contain sufficientRNA for microarray analysis, as we were able to analyze the mRNAs inwhole genome porcine microarrays. We obtained endoarterial biopsies andmeasured pulmonary arterial pressure (PAP) at baseline prior to surgery,and at approximately 7, 21, 60 and 180 days post-PAH surgery fromseveral animals. Porcine whole genome expression values were obtainedfor biological replicates with 2 samples from each time point. Thesereplicates produced 5 sets of high quality replicated expression data(baseline, day 7, day 21, day 60 and day 180; see Table 1 for PAP data).Downstream data analysis was carried out using commercial (Ingenuity;GeneSpring) and free/open source software (R; Bioconductor; GSEA). Meanexpression values were obtained for each gene by averaging the geneexpression values of the two biopsies at each timepoint. The resultinggene expression mean values were used to calculate fold changes betweenday 7, 21, 60 and day 180 gene expression relative to baseline.

Validity of the model was confirmed by examining the gene expressionchanges for selected genes previously found to be dysregulated in PAH(Table 2). Endothelin 1 and protein-tyrosine kinase Tie2 both displayedupregulation in accordance with explanted tissue from IPAH transplantrecipients (Dewatcher et al 2006), and platelet-derived growth factorreceptor alpha, serotonin receptors 2B and 1D, calmodulin, transcriptionfactor STAT5b, voltage-dependent anion channels 1, 2 and 3, and RAS p21protein activator 1 also increased in our model while tumor necrosisfactor and plasminogen activator inhibitor-1 were found to bedownregulated in our model in a similar fashion with IPAH explant tissueresults (Fantozzi et al 2005). Survivin was upregulated in our model ina similar fashion to published findings (McMurtry et al 2005), and FYNand VAV-1 oncogenes, requiem homolog, inward rectifier K+ channel, andchloride channel 1 also increased while DEAD/H box polypeptide 3 andangiopoetin 1 displayed decreased expression in agreement with patientfindings (Geraci et al 2001). We also observed decreased expression ofperoxisome proliferator-activated receptor gamma (Ameshima et al 2003),and downregulated vascular endothelial growth factor B (Louzier et al2003) in correspondence with previous results. The concordance betweengenes previously found to be aberrant in published PAH studies andaltered gene expression in our model attest to the validity andpotential usefulness of gene expression data derived from endoarterialbiopsies. The time dependent nature of gene expression dysregulationfound in our model further demonstrates the utility of obtainingendoarterial biopsies at multiple time points in PAH progression.

While several of these genes have been previously associated with PAH(for example, KCBN1, CASP3, TLR4, IL1B, IL6, HMGCR, TOF1, FYN, PRKCA,EDNRB, PDGFRA, and HRT2B), several have not (for example, HSPE, YES1,CFTR, MAOA, MAOB, and CACND21), raising the intriguing possibility thatknown existing drugs that target upregulated genes previouslyunassociated with PAH may be effective in treatment of the disease.

Example III Identification of Dysregulated microRNA During theProgression of PAH

Endoarterial biopsy samples percutaneously obtained during theprogression of PAH were analyzed to correlate changes in microRNAexpression to disease progression.

microRNA Expression Data Analysis

Data analysis was done in three stages. First, expression intensitieswere calculated for each miRNA probed on the array for allhybridizations (12 in total) using illumine's Beadstudio Version 3.0software. Second, intensity values were quality controlled andnormalized: quality control was carried out by using the illuminaBeadstudio detection P-value set to <0.05 as a cutoff. This removedmiRNAs which were effectively absent from the arrays (that is, werenever detected). After this step, the initial 1145 miRNAs were reducedto 1094. All the arrays were then normalized using thenormalize.quantiles routine from the Affy package in Bioconductor. Thisprocedure accounted for any variation in hybridization intensity betweenthe individual arrays

Finally, these normalized data were imported into GeneSpring andanalysed for differentially expressed miRNAs. The groups of biologicalreplicates were described to the software and significantlydifferentially expressed genes determined on the basis of Welch t-testsand fold difference changes in expression level. The determination ofmiRNA targets genes was done using a publicly available database ofmiRNA target sequences and a specially written PERL programming script.

miRNA Pressure Related Analysis

The data was also looked at to reflect the stages of the disease (basedon blood pressure and flow rates), as opposed to the time point or theindividual pigs. Three groups were defined (1) Normal (baseline); (2)High Flow Low Pressure ‘HFLP’ and (3) High Flow High Pressure ‘HFHP’(see Table 11). The groups were compared back to the baseline and thestatistically significantly differentially regulated miRNAs determined(Tables 12, 13, 14 & 15).

Using illumina microRNA expression microarrays, fluctuations in thelevel of expression of ˜1200 microRNAs were determined during the onsetand progression of PAH. Porcine and Homo sapiens miRNA sequences arevery often highly conserved. Expression comparisons were done on atimepoint basis, taking in account the available replicates and thestatistical significance of the expression changes. The data was alsolooked at to reflect the stages of the disease (based on blood pressureand flow rates), as opposed to the time point or the individual pigs.Three groups were defined (1) Normal (baseline); (2) High Flow LowPressure ‘HELP’ and (3) High Flow High Pressure ‘HFHP’. The groups werecompared back to the baseline and the statistically significantlydifferentially regulated miRNAs determined.

Finding Micro RNAs with Potential as Therapeutic Targets

The messenger RNA expression data set was analysed looking forexpression changes in sets of genes with known target sites forparticular miRNAs. miRNAs are known to negatively regulate geneexpression at the level of translation by binding to upstream regions ofmRNA and blocking events required for translation of the mRNA intoprotein. This was again done using Gene Set Enrichment Analysis (GSEA)and the publicly available miRNA genesets. “Cross-talk” is seen betweenthe messenger RNA gene expression changes and the microRNA expressionchanges. The messenger RNA expression analysis directly revealed thedifferential expression of groups of genes competent to be regulated bythese miRNA.

Example IV Personalizing Therapeutic Regimens for Vascular-BasedDiseases

The use of gene expression data to shape individual drug therapies hasbeen postulated as the next phase in personalized medicine. Thebioinformatic processing of an individual's gene expression data can beused to generate a ranked list of therapies suitable for thatindividual. PAH disease pathology varies greatly over time, and is alsolikely to be specific for particular individuals. The analysis of theRNA in the PAH biopsy samples allows therapies to be tailored to theindividual at that particular stage of the diseases progression.

The genes and biochemical pathways changing the most at the level ofgene expression can be determined by comparing the PAH biopsy samples toa baseline control of normal healthy vasculature tissue. Observationsshow time-dependent extensive changes in gene expression with theprogression of PAH. Known targets for approved PAH therapeutics can beseen Up-regulated in the diseased state.

Drug therapies can be ranked by using the known targets of drugs asgenesets. These drug signature lists can then be used in a process suchas Gene Set Enrichment Analysis, or KS statistics. KS Statistics returnsa score for how well ranked a particular drug would be for a particularpatient.

A drug is represented as the set of its known target genes; this can bein the dozens for some bioactive compounds. Genesets for ˜2000 drugswere assembled. KS Statistics yields a value (‘KS score’) representingthe positional distribution of the set of query genes (here, the drugtargets) within an ordered list of genes (genes induced in PAH). Theordered list is produced by looking at the fold change in a mRNAsexpression between time X and the baseline, and sorting on this value.The gene with the greatest fold change is ranked as #1, second greatestfold change is ranked as #2, etc. KS score is computed in accordancewith the Kolmogorov-Smirnov non-parametric rank statistic where X is thenumber of genes in the query gene set, Z is the number of genes in theordered list, and Y=Z−X. A suitable baseline is generated using geneexpression from artery samples from non-diseased controls. These samplescan be obtained surgically, percutaneously or post-mortem.

This process can be repeated for all the PAH time points and theresulting table of KS scores for each drug hierarchically clustered.This reveals which drugs are potentially of the greatest therapeuticvalue for a patient.

This supports the idea of achieving personalized treatments forvascular-based diseases by generating individualized drug prescriptionsbased on the bioinformatic processing of gene expression data fromendoarterial biopsy samples obtained from diseased arteries. Similarly,this enables personalized treatments for vascular-based diseases bygenerating lists of dysregulated microRNA from the bioinformaticprocessing of microRNA expression data from endoarterial biopsy samplesfrom diseased arteries.

TABLE 1 Pulmonary arterial pressures obtained during endoarterial biopsycatheterization for biopsy samples used in microarray analysis.Pulmonary Arterial Pressure mmHg Biopsy Sample Systolic Diastolic MeanBaseline Pig #9 22 11 17 Baseline Pig #10 25 16 18 Day 21 Pig #2 95 6682 Day 21 Pig #6 41 26 33 Day 60 Pig #6 87 59 74 Day 60 Pig #5 49 27 38

TABLE 2 Selected genes previously associated with PAH similarlydysregulated in the porcine model. Fold Fold Fold Fold Change ChangeChange Change Day Gene Day Day Day 180/ Symbol Name Baseline Day 7 Day21 Day 60 Day 180 7/Base 21/Base 60/Base Base VAV1 vav 1 oncogene 32.5621.65 237.16 138.29 15.39 −1.50 7.28 4.25 −2.12 RASA1 RAS p21 protein73.23 388.68 280.27 704.56 361.25 5.31 3.83 9.62 4.93 activator 1 TIE2protein-tyrosine 20.92 2.59 32.46 702.68 218.34 −8.08 1.55 33.59 10.44kinase Tie2 FYN fyn proto- 43.33 180.38 404.77 531.03 166.17 4.16 9.3412.26 3.83 oncogene VDAC1 voltage-dependent 1176.57 2350.33 6629.763144.14 2277.10 2.00 5.63 2.67 1.94 anion channel 1 PDGFRAplatelet-derived 69.46 152.75 10.45 611.81 18.80 2.20 −6.64 8.81 −3.69growth factor receptor alpha 5-HT2B serotonin 2B 49.96 19.03 166.45142.91 488.77 −2.63 3.33 2.86 9.78 receptor KCNJ2 inwardly 389.66 83.231059.11 212.29 84.28 −4.68 2.72 −1.84 −4.62 rectifying potassium channelKIR6.1 5-HT1D serotonin 1D 14.17 42.48 8.32 61.48 4.95 3.00 −1.70 4.34−2.86 receptor DPF2 requiem, 140.95 123.89 140.90 195.55 93.92 −1.14−1.00 1.39 −1.50 apoptosis response zinc finger gene VDAC2 Voltage-5683.09 2665.62 1620.37 4940.32 3643.38 −2.13 −3.51 −1.15 −1.56dependent anion channel 2 STAT5B signal transducer 469.40 571.47 1327.53808.09 626.07 1.22 2.83 1.72 1.33 and activator of transcription 5b AGPTangiopoietin 1 17.825026 50.240685 11.806807 70.12715 3.4479218 2.82−1.51 3.93 −5.17 BIRC5 apoptosis 169.33 751.37 140.45 31.26 44.69 4.44−1.21 −5.42 −3.79 inhibitor survivin VDAC3 voltage-dependent 4092.99750.86 5013.26 959.72 2018.55 −5.45 1.22 −4.26 −2.03 anion channel 3PLANH1 plasminogen 27760.742 43007.71 23685.375 28771.838 36086.305 1.55−1.17 1.04 1.30 activator inhibitor I PPARG peroxisome 177.80 12.8618.96 194.20 62.40 −13.83 −9.38 1.09 −2.85 proliferator- activatedreceptor gamma 2 CALM1 Calmodulin 3092.78 2436.23 867.25 1401.38 2252.81−1.27 −3.57 −2.21 −1.37 APOE apolipoprotein E 358.91 206.34 94.35 129.60288.79 −1.74 −3.80 −2.77 −1.24

TABLE 3 Day 7 prescription. Fold Fold Fold Fold Change Change ChangeChange D 7/ D 21/ D 60/ D 180/ Gene Probe ID Name Base Base Base BaseSymbol DRUGS Ssc.11018.1.A1_at Mitogen-activated protein 19.80 −5.02−17.27 −20.43 MAPK14 SCIO-469, RO-3201195 kinase 14 Ssc.15986.1.S1_atInsulin receptor 29.28 −16.85 −17.70 −19.01 INSR insulin, insulinaspart, insulin glulisine, insulin lispro, insulin glargineSsc.873.1.S1_at Cell division control protein 2 27.38 −2.37 −4.66 −7.76CDC2 flavopiridol Ssc.29928.1.A1_at Histone deacetylase 11 (HD11) 21.56−3.17 −2.91 −10.50 HDAC11 tributyrin, FXD101, pyroxamide, vorinostat,FR901228 Ssc.100.1.S1_at Tumor necrosis factor 18.41 −1.70 −9.62 −3.15TNF adalimumab, etanercept, precursor (TNF-alpha) infliximab, CDF870,golimumab, thalidomide Ssc.19672.1.S1_at RAC-alpha serine/threonine-17.77 1.25 −19.62 −2.11 AKT1 enzastaurin protein kinaseSsc.14475.3.S1_a_at Peroxisome proliferator 13.83 −9.38 1.09 −2.85 PPARGrosiglitatone, GI262570, activated receptor gamma pioglitozone,tesaglitazar, (PPAR-gamma) troglitazone Ssc.14326.1.A1_atMitogen-activated protein 12.63 1.56 −1.80 −7.24 MAPK13 SCIO-469 kinase13 Ssc.25843.1.S1_at Chloride channel protein 2 11.77 −17.04 −21.97−9.92 CLCN2 lubiprostone (ClC-2 Ssc.16201.1.A1_at Metabotropic glutamate10.79 −35.68 −33.34 −47.92 GRM7 fasoracetam receptor Ssc.11381.1.S1_atInterferon-alpha/beta receptor 10.45 8.08 2.61 −1.30 IFNAR1 interferonbeta-1a, interferon alpha chain alfa-2b, interferon alfacon-1,PEG-interferon alfa-2a, interferon alfa-2a/ribavirin, pegintron,interferon beta-1b, IFNA2A Ssc.5371.1.S1_a_at DNA polymerase epsilonsubunit 10.16 1.68 −1.37 −3.14 POLE2 gemcitabine B (DNA polymerase IIsubunit B) Ssc.14471.1.S1_at B-lymphocyte antigen CD19 9.54 3.30 −10.323.04 CD19 combotox, HD37-dgRTA, MT103 Ssc.24856.1.A1_atphosphodiesterase 11A; cyclic 9.36 −2.70 −3.68 −2.68 PDE11A dyphylline,nitroglycerin, nucleotide phosphodiesterase aminophylline, dipyridamole,11A1 tolbutamide, tadalafil, theophylline, pentoxifyllineSsc.189.1.S1_at Diacylglycerol O- 9.16 −4.21 −36.07 −24.06 DGAT1 omacoracyltransferase 1 Ssc.16186.1.S1_at T-cell surface glycoprotein 9.003.12 2.12 −5.66 CD3E visilizumab, MT103, muromonab- CD3 epsilon CD3Ssc.15601.1.A1_s_at Interleukin-1 beta precursor 8.18 4.65 −14.71 −2.84IL1B IL-1 trap (IL-1 beta) Ssc.5538.1.S1_at Carbonic anhydrase II 8.091.39 −2.25 −1.35 CA2 methazolamide, (Carbonate dehydratase II)hydrochlorothiazide, (CA-II) (Carbonic anhydrase acetazolamide, C)]trichloromethiazide, dorzolamide, chlorothiazide, dorzolamide/timolol,brinzolamide, chlorthalidone, benzthiazide, sulfacetamide, topiramateSsc.113.1.S1_at Interleukin-1 alpha (IL-1 8.01 −2.65 −1.59 −7.73 IL1AIL-1 trap alpha) Ssc.2895.1.S1_at Serine/threonine-protein 7.48 −2.02−2.45 −1.81 AURKB AZD-1152 kinase Ssc.8219.1.A1_at Histone deacetylase 8(HD8) 7.21 −2.18 −12.09 −29.63 HDAC8 tributyrin, PXD101, pyroxamide,vorinostat, FR 901228 Ssc.13473.1.A1_at Ceramide glucosyltransferase7.13 −2.88 −4.17 −6.14 UGCG N- butyldeoxygalactonojirimycin,N-butyldeoxynojirimycin Ssc.14129.1.A1_at 4-aminobutyrate 6.91 2.56−21.17 −3.35 ABAT valproic acid aminotransferase, mitochondrial (GABAtransaminase) Ssc.15379.1.S1_at diacylglycerol O- 6.60 −1.51 −3.49 −2.13DGAT2 omacor acyltransferase homolog 2; GS1999full Ssc.15830.1.A1_atRetinoic acid receptor beta 6.60 −3.28 −1.83 −1.10 RARB etretinate,adapalene, 13-cis- retinoic acid, tazarotene, acitretin, retinoic acid,9- cis-retinoic acid, fenretinide Ssc.17928.1.A1_at helicase (DNA) B;helicase B 6.40 −2.65 −4.38 −1.06 HELB epirubicin Ssc.19673.1.S1_atT-cell surface glycoprotein 6.40 2.70 2.03 −11.77 CD3D visilizumab,MT103 CD3 delta Ssc.17222.1.A1_at mucin 1, transmembrane; 6.31 −6.10−5.94 −13.48 MUC1 HuHMFG1 Ssc.55.1.S1_at Epidermal growth factor 6.09−5.46 −4.68 −4.52 EGFR cetuximab, AEE 788, receptor panitumumab,BMS-599626, ARRY- 334543, XL647, canertinib, gefitinib, HKI-272, PD153035, lapatinib, vandetanib, erlotinib Ssc.19059.1.A1_at Type-1angiotensin II receptor 5.57 −2.57 1.50 −11.08 AGTR1amlodipine/olmesartan (AT1) (AT1AR medoxomil,losartan/hydrochlorothiazide, valsartan/hydrochlorothiazide, candesartancilexetil, olmesartan medoxomil, irbesartan, losartan potassium,telmisartan, eprosartan, candesartan cilexetil/hydrochlorothiazide,hydrochlorothiazide/irbesartan, eprosartan/hydrochlorothiazide,hydrochlorothiazide/telmisartan, hydrochlorothiazide/olmesartanmedoxomil, valsartan Ssc.16162.1.S1_at 4-hydroxyphenylpyruvate 5.43−8.93 −8.65 −3.84 HPD nitisinone dioxygenase Ssc.27603.1.S1_atEndothelin B receptor 5.30 −3.27 15.99 1.23 EDNRB bosentan, sitaxsentan,atrasentan Ssc.16333.1.A1_at Multidrug resistance protein 1 4.94 −2.99−3.50 −22.89 ABCB1 XR9576, OC 144-093, valspodar Ssc.12769.1.A1_atAmiloride-sensitive cation 4.82 −13.74 −9.59 −10.72 ACCN1 amiloride,channel 1, neuronal amiloride/hydrochlorothiazide Ssc.17155.1.At_atheparanase; heparanase-1 4.81 5.38 2.98 −1.83 HPSE heparanase inhibitorPI-88 Ssc.15933.1.S1_s_at Cytotoxic T-lymphocyte protein 4.76 −5.14−6.63 −26.39 CTLA4 ipilimumab, ticilimumab 4 (Cytotoxic T-lymphocyte-associated antigen 4) (CTLA-4) (CD152 antigen) Ssc.15965.1.S1_at Inwardrectifier potassium 4.68 2.72 −1.84 −4.62 KCNJ2 nicorandil, amiodaronechannel 2 (IRK1) Ssc.26351.1.S1_at cAMP-specific 3′,5′-cyclic 4.67 4.993.61 −1.15 PDE4D dyphylline, nitroglycerin, phosphodiesterase 4Darofylline, tetomilast, L 869298, aminophylline, anagrelide, cilomilast,milrinone, rolipram, dipyridamole, L-826,141, roflumilast, tolbutamide,theophylline, pentoxifylline, caffeine Ssc.15990.1.A1_at Retinoic acidreceptor RXR- 4.42 −4.18 −18.45 −24.58 RXRA bexarotene, retinoic acid,9- alpha cis-retinoic acid Ssc.2605.1.A1_at Protein farnesyltransferase4.39 −2.62 −7.00 −2.74 FNTB lonafarnib, tipifarnib betaSsc.30373.1.A1_at cGMP-specific 3′,5′-cyclic 4.27 1.52 2.34 4.09 PDE5Adyphylline, nitroglycerin, DA- phosphodiesterase 8159, aminophylline,sildenafil, dipyridamole, aspirin/dipyridamole, vardenafil, tolbutamide,tadalafil, theophylline, pentoxifylline Ssc.19233.1.S1_at Collagen alpha2(IX) chain 4.23 −1.14 −22.83 −2.12 COL9A2 collagenase Ssc.1147.1.A1_atLipoprotein lipase 4.05 −5.49 3.78 −8.08 LPL nicotinic acid,lovastatin/niacin Ssc.13160.1.A1_at Voltage-dependent L-type 4.03 −4.75−1.11 −2.77 CACNA1F MEM-1003, mibefradil, calcium channel alpha-1Fbepridil, nisoldipine, subunit isradipine, nicardipine Ssc.12748.1.A1_atCatechol O-methyltransferase, 4.03 −3.20 −5.82 −21.93 COMTcarbidopa/entacapone/levodopa, membrane-bound form BIA-3-202, tolcapone,entacapone Ssc.24986.1.S1_at Aldehyde dehydrogenase 1A1 4.00 −3.76 −2.17−9.20 ALDH1A1 disulfiram, chlorpropamide Ssc.15972.1.S1_at Peroxisomeproliferator 3.83 −1.07 −2.73 −1.60 PPARD GW501516 activated receptordelta (PPAR-delta) Ssc.24509.1.A1_at Gamma-aminobutyric-acid 3.76 −1.28−1.98 −1.23 GABRP alphadolone, sevoflurane, receptor pi subunitisoflurane, isoniazid, felbamate, etomidate, halothane,fluoxetine/olanzapine, eszopiclone, zolpidem, lorazepam, olanzapine,zaleplon, secobarbital, phenobarbital, pentobarbital, desflurane,methoxyflurane, enflurane Ssc.7176.1.A1_at C—X—C chemokine receptor type3.74 10.91 8.15 1.68 CXCR4 JM 3100 4 (CXC-R4) ( Ssc.6570.1.S1_atDelta-aminolevulinic acid 3.71 −3.43 −3.05 −1.66 ALADdelta-aminolevulinic acid dehydratase] Ssc.17485.1.S1_at Guanylatecyclase soluble, 3.57 −38.82 −1.77 −7.04 GUCY1A2 nitroglycerin,isosorbide-5- alpha-2 chain mononitrate, isosorbide dinitrate,nitroprusside, isosorbide dinitrate/hydralazine Ssc.26200.1.S1_atThyroid hormone receptor beta-1 3.49 −1.56 7.96 2.52 THRB3,5-diiodothyropropionic acid, amiodarone, thyroxine, L-triiodothyronine Ssc.9595.1.S1_at Beta platelet-derived growth 3.48−3.60 1.40 1.65 PDGFRB dasatinib, sunitinib, factor receptor axitinib,KRN-951, imatinib, sorafenib, becaplermin Ssc.108.1.S1_at Oxytocinreceptor (OT-R) 3.44 −8.53 −16.69 −4.47 OXTR TT-235 Ssc.15801.1.A1_atProtein kinase C, beta 3.36 6.36 3.53 −4.98 PRKCB1 enzastaurin,ruboxistaurin Ssc.27928.1.S1_at Opioid growth factor receptor 3.34 −3.33−2.89 −3.51 OGFR enkephalin, methionine (OGFr) Ssc.12791.1.A1_at3-hydroxy-3-methylglutaryl- 3.27 2.77 1.77 −2.56 HMGCRaspirin/pravastatin, coenzyme A reductase (HMG-CoA lovastatin/niacin,reductase ezetimibe/simvastatin, amlodipine/atorvastatin, fluvastatin,cerivastatin, atorvastatin, pravastatin, simvastatin, lovastatin,rosuvastatin Ssc.7933.1.A1_at Cell division protein kinase 8 3.26 −1.63−1.78 −3.05 CDK8 flavopiridol Ssc.11147.1.S1_at Aldehyde dehydrogenase,3.18 1.13 2.00 −1.68 ALDH2 disulfiram, chlorpropamide mitochondrial(ALDH class 2) (ALDHI) (ALDH-E2) Ssc.19608.1.S1_at Retinoic acidreceptor RXR- 3.15 −1.39 −1.73 −3.19 RXRG bexarotene, retinoic acid, 9-gamma cis-retinoic acid Ssc.29260.1.A1_at Granulocyte colony stimulating3.15 −2.50 −4.36 −4.68 CSF3R pegfilgrastim, filgrastim factor receptor(G-CSF-R) (CD114 antigen)] Ssc.22797.1.S1_at DNA topoisomerase II, beta3.15 −1.87 1.02 −2.91 TOP2B novobiocin, etoposide, CPI- isozyme 0004Na,pixantrone, becatecarin, elsamitrucin, AQ4N, BN 80927, tafluposide,mitoxantrone, norfloxacin, dexrazoxane, tirapazamine, TAS- 103, XK469,gatifloxacin, valrubicin, gemifloxacin, moxifloxacin, nemorubicin,nalidixic acid, epirubicin, doxorubicin, daunorubicin Ssc.16121.1.A1_atCorticotropin releasing factor 3.03 −4.50 −17.00 −4.36 CRHR1 Crh,CRA0165, CRA1001, receptor 1 SSR125543A Ssc.12630.1.A1_atSodium/potassium-transporting 2.97 2.81 −7.30 −2.03 ATP1A1 digoxin,omepratole, ATPase alpha-1 chain ethacrynic acid, perphenazineSsc.13254.1.A1_at Metabotropic glutamate 2.95 −15.40 −9.66 −3.57 GRM8fasoracetam receptor 8 Ssc.30888.1.S1_at Voltage-dependent L-type 2.92−2.72 1.90 −7.82 CACNA1D MEM-1003, mibefradil, calcium channel alpha-1Dbepridil, nisoldipine, isradipine, nicardipine Ssc.9565.1.S1_atInterferon-gamma receptor 2.92 1.63 1.41 −1.23 IFNGR1 interferongamma-1b alpha Ssc.15880.1.S1_at Cysteinyl leukotriene receptor 2.861.14 −2.12 −3.42 CYSLTR2 montelukast, zafirlukast 2 (CysLTR2)Ssc.2753.1.S1_at Serine/threonine-protein 2.77 −4.42 −7.50 −4.52 PLK1 BI2536 kinase PLK1 Ssc.16123.1.A1_at cAMP-specific 3′,5′-cyclic 2.75 −3.97−3.49 −1.46 PDE4A arofylline, tetomilast, LB69298, phosphodiesterase 4Aanagrelide, cilomilast, milrinone, rolipram, L-826,141, amrinone,roflumilast, pentoxifylline, caffeine Ssc.11383.1.A1_at Glutamatereceptor 3 2.61 1.85 −1.87 −2.43 GRIA3 talampanel, Org 24448, LY451395,tezampanel Ssc.14403.1.S1_at Sodium/potassium-transporting 2.61 −1.95−8.51 −6.43 ATP1A2 digoxin, omeprazole, ATPase alpha-2 chain ethacrynicacid, perphenazine Ssc.21754.1.A1_at Collagen alpha 1(VI) chain 2.57−47.00 −5.79 −4.37 COL6A1 collagenase Ssc.6498.1.A1_at Mitogen-activatedprotein 2.41 −10.79 −5.78 −3.26 MAPK12 SCIO-469 kinase 12(Mitogen-activated protein kinase p38 gamma) Ssc.16167.1.S1_atRho-associated protein kinase 1 2.40 2.32 2.83 3.00 ROCK1 fasudil,Y-27632 Ssc.12781.1.A1_at Toll-like receptor 4 2.39 1.83 −1.52 −6.10TLR4 TAK-242 Ssc.29366.1.A1_at DNA topoisomerase I 2.37 −2.30 −2.87−10.72 TOP1 elsamitrucin, T 0128, CT-2106, BN 80927, tafluposide,TAS-103, beta-lapachone, irinotecan, topotecan, 9-amino-20-camptothecin, rubitecan, gimatecan, karenitecin Ssc.14485.1.S1_atParathyroid 2.28 −1.62 −3.40 −6.83 PTHR1 teriparatidehormone/parathyroid hormone- related peptide receptor Ssc.12238.1.A1_atCysteinyl leukotriene receptor 2.28 −1.73 −1.34 −6.96 CYSLTR1 zeneca ZD3523, montelukast, 1 (CysLTR1) zafirlukast Ssc.3607.1.S1_atInterferon-alpha/beta receptor 2.28 4.65 1.11 −1.56 IFNAR2 interferonbeta-1a, interferon beta chain alfa-2b, interferon alfacon-1,PEG-interferon alfa-2a, interferon alfa-2a/ribavirin, pegintron,interferon beta-1b, IFNA2A Ssc.2548.1.S1_at DNA polymerase epsilon p17]2.27 1.93 −1.67 −1.21 POLE3 gemcitabine Ssc.19706.1.A1_atMitogen-activated protein 2.25 −4.27 −2.31 −4.98 MAPK8 aplidine kinase 8Ssc.15382.1.S1_at Cannabinoid receptor 2 (CB2) 2.22 3.48 −1.37 −4.69CNR2 BAY 38-7271, delta-9- (CB-2) (CX5) tetrahydrocannabinolSsc.4756.1.A1_at Adenosine A3 receptor 2.15 2.10 1.88 −1.81 ADORA3adenosine, dyphylline, aminophylline, clofarabine, theophylline,caffeine Ssc.23261.1.A1_at Trifunctional purine 2.15 −3.54 −3.66 −5.67GART LY231514 biosynthetic protein adenosine-3 Ssc.27293.1.A1_atHypoxanthine-guanine 2.15 −1.16 1.63 −7.14 HPRT1 6-mercaptopurine,thioguanine, phosphoribosyltransferase azathioprine Ssc.14476.1.S1_atInterleukin-2 receptor alpha 2.07 −8.52 −8.73 −5.00 IL2RA LMB-2,daclizumab, basiliximab, aldesleukin, denileukin diftitoxSsc.27232.1.S1_at Succinate semialdehyde 2.06 1.12 −2.84 −5.73 ALDH5A1valproic acid dehydrogenase, mitochondrial Ssc.10142.1.A1_atDihydropyrimidine 2.06 2.17 1.13 −2.68 DPYD eniluracil dehydrogenase[NADP+] Ssc.1908.1.S1_at FKBP-rapamycin associated 1.99 1.13 −1.88 −1.46FRAP1 AP23573, temsirolimus, protein (FRAP) tacrolimus, everolimusSsc.204.1.S1_at Cytochrome P450 3A4 1.97 −3.35 2.16 −1.42 CYP3A4ketoconazole Ssc.18459.1.S1_at Amiloride-sensitive sodium 1.97 −2.411.43 −1.93 SCNN1A triamterene/hydrochlorothiazide, channel alpha-amiloride, amiloride/hydrochlorothiazide, triamterene Ssc.24889.1.S1_atArachidonate 12-lipoxygenase, 1.97 2.83 −1.18 −2.78 ALOX12sulfasalazine, balsalazide, 5- 12S-type aminosalicylic acid, masoprocol,verteporfin Ssc.15748.2.S2_at T lymphocyte activation 1.95 −1.24 1.54−3.12 CD80 abatacept antigen CD80 Ssc.5826.1.A1_at Macrophage colonystimulating 1.93 −4.97 −13.18 1.61 CSF1R sunitinib factor I receptor(CD115 antigen) Ssc.15822.1.S1_at Coagulation factor V 1.92 3.76 1.89−1.75 F5 drotrecogin alfa Ssc.9262.1.A1_at Histamine H1 receptor 1.91−4.10 −3.91 −1.86 HRH1 nitisinone Ssc.62.2.S1_a_at Interleukin-6 (IL-6)( 1.89 −6.32 2.77 −1.04 IL6 tocilizumab Ssc.14258.1.S1_at Amyloid betaA4 protein 1.87 3.33 1.34 −1.02 APP AAB-001 Ssc.15878.1.S1_atSerine/threonine protein 1.85 3.22 3.62 −1.49 PPP3CA ISAtx-247,tacrolimus, phosphatase 2B pimecrolimus, cyclosporin A Ssc.19379.1.A1_atVoltage-dependent L-type 1.83 −1.34 1.07 −3.27 CACNA1C clevidipine,MEM-1003, calcium channel alpha-1C amlodipine/olmesartan subunitmedoxomil, amlodipine/benazepril, diltiazem, verapamil, mibefradil,bepridil, enalapril/felodipine, amlodipine/atorvastatin, nisoldipine,isradipine, felodipine, nimodipine, nitrendipine, amlodipine,nicardipine, nifedipine, trandolapril/verapamil, diltiazem/enalaprilSsc.10215.1.A1_at High-affinity cAMP-specific 1.83 1.12 −8.48 −15.51PDE8A dyphylline, nitroglycerin, and IBMX-insensitive 3′,5′-aminophylline, anagrelide, cyclic phosphodiesterase 8A milrinone,dipyridamole, tolbutamide, theophylline, pentoxifyllineSsc.20944.1.S1_at Carbonic anhydrase XIV 1.82 −3.49 −5.34 −12.64 CA14methazolamide, hydrochlorothiazide, acetazolamide, trichloromethiazide,chlorothiazide, chlorthalidone, benzthiazide, sulfacetamide, topiramateSsc.4125.1.A1_at Histone deacetylase 5 (HD5) 1.82 −4.64 −4.18 −2.74HDAC5 tributyrin, PXD101, pyroxamide, vorinostat, FR 901228Ssc.9272.1.S1_at Tumor-associated calcium 1.81 3.94 176.50 2.07 TACSTD1tucotuzumab celmoleukin signal transducer 1 (EPCAM antigen)Ssc.6301.1.S1_at Aromatic-L-amino-acid 1.76 1.80 −4.91 −1.88 DDCcarbidopa/entacapone/levodopa, decarboxylase carbidopa/levodopa, S(−)-carbidopa, L-dopa Ssc.15995.1.S1_at Potassium voltage-gated 1.74 −26.30−13.45 −2.79 KCNE1 nicorandil, amiodarone, channel subfamily E member 1azimilide Ssc.7581.1.A1_at FL cytokine receptor precursor 1.69 1.04−1.81 1.01 FLT3 CHIR-258, sorafenib, lestaurtinib, CGP 41251Ssc.26325.1.S1_at Cystic fibrosis transmembrane 1.60 −5.71 4.77 −8.99CFTR SP 303 conductance regulator (CFTR) Ssc.19691.1.S1_atPlatelet-activating factor 1.59 1.16 3.01 1.47 PLA2G7 darapladibacetylhydrolase Ssc.24714.1.A1_at Excitatory amino acid 1.58 −2.29 −7.61−3.45 SLC1A2 riluzole transporter 2 (Sodium- dependentglutamate/aspartate transporter 2) Ssc.22477.1.S1_at Collagen alpha1(IV) chain 1.58 −5.08 −1.78 1.04 COL4A1 collagenase Ssc.227.1.S1_atPotassium-transporting ATPase 1.56 −5.89 −51.53 −15.60 ATP4B ilaprazole,TAK-390MR, beta tenatoprazole, AGN 201904, AR- H047108, esomeprazolemagnesium, omeprazole, lansoprazole, amoxicillin/clarithromycin/lansoprazole, rabeprazole, pantoprazole Ssc.30147.1.A1_at Fibroblast growthfactor 1.56 1.13 −1.05 −1.18 FGFR2 palifermin receptor 2Ssc.9523.1.A1_at Methylated-DNA--protein- 1.55 −1.17 3.35 1.47 MGMTO6-benzylguanine cysteine methyltransferase Ssc.26466.1.A1_at Integrinbeta-3 (CD61 antigen 1.55 −1.49 −4.11 −2.73 ITGB3 TP 9201, EMD121974,tirofiban Ssc.5592.1.S1_at Protein 1.49 −3.49 −2.81 −3.68 FNTAlonafarnib, tipifarnib farnesyltransferase/geranylger anyltraneferasetype I alpha Ssc.17986.1.A1_at Poly [ADP-ribose] polymerase-1 1.47 −6.14−4.64 −5.80 PARP1 INO-1001 Ssc.11051.1.S1_at Cell division proteinkinase 4 1.44 −7.67 −4.96 23.75 CDK4 PD-0332991, flavopiridolSsc.20818.1.S1_at Interleukin-2 receptor beta 1.43 6.35 −1.17 −5.23IL2RB humanized MiK-Beta-1, chain aldesleukin, denileukin diftitoxSsc.16489.1.S1_at Interleukin-7 receptor alpha 1.42 2.34 1.86 −6.31 IL7Rrecombinant human interleukin-7 chain Ssc.10287.1.A1_at Transforminggrowth factor 1.41 −4.54 1.43 1.67 TGFB2 AP-12009 beta 2Ssc.14375.1.A1_at ribonucleotide reductase M2 B 1.40 −2.19 −5.17 −2.28RRM2B triapine, hydroxyurea Ssc.16823.1.S1_at P2Y purinoceptor 12(P2Y12) 1.38 1.19 1.41 1.11 P2RY12 prasugrel, AZD 6140 (P2Y12 plateletADP receptor) (Ticagrelor), clopidogrel (P2Y(ADP)) Ssc.11164.1.A1_at DNApolymerase gamma subunit 1 1.37 −1.33 −3.67 −3.60 POLG stavudine,vidarabine, zalcitabine Ssc.10219.1.A1_at Excitatory amino acid 1.361.24 −3.38 −1.03 SLC1A6 riluzole transporter 4 Ssc.3815.1.S1_at RAC-betaserine/threonine- 1.35 −3.13 −3.28 −3.19 AKT2 enzastaurin protein kinaseSsc.19619.1.S1_at Proto-oncogene tyrosine- 1.35 −1.51 −3.32 −2.41 LCKdasatinib protein kinase LCK Ssc.2926.1.S1_at Heme oxygenase 2 1.34−1.43 −4.13 −1.81 HMOX2 tin mesoporphyrin Ssc.11171.1.S1_at Adenosinedeaminase 1.32 −2.04 −3.23 1.12 ADA pentostatin, vidarabineSsc.16621.1.A1_at Excitatory amino acid 1.27 −7.18 −3.04 −8.29 SLC1A1riluzole transporter 3 Ssc.11549.1.A1_at Dual specificity mitogen- 1.25−33.67 −11.33 −6.48 MAP2K1 PD 0325901 activated protein kinase kinase 1Ssc.6356.1.S1_at Ornithine decarboxylase 1.24 −1.36 −1.74 −1.84 ODC1tazarotene, eflornithine Ssc.15999.1.A1_at Vascular endothelial growth1.24 1.24 18.52 −11.02 KDR AEE 788, sunitinib, AZD 2171, factor receptor2 (VEGFR-2) pasopanib, XL647, CEP 7055, BMS-582664, KRN-951, vatalanib,sorafenib, vandetanib, pegaptanib Ssc.9669.1.S1_at Cell division proteinkinase 5 1.21 −2.68 −17.06 −1.65 CDK5 flavopiridol Ssc.115.1.S1_s_atHeme oxygenase 1 1.18 −2.09 −3.40 −3.55 HMOX1 tin mesoporphyrinSsc.17224.1.S1_at Toll-like receptor 8 1.17 6.49 3.13 −1.52 TLR8resiquimod Ssc.8046.1.A1_at peptidylprolyl, isomerase A 1.16 −1.08 1.391.26 PPIA M-methyl-4-Ile-cyclosporin isoform 1 Ssc.7297.1.S1_at Amineoxidase [flavin- 1.16 6.42 7.02 −1.13 MAOB safinamide, ladostigil,containing] B (MAO-B) rasagiline, selegiline, dextroamphetamine,procainamide, tranylcypromine, phenelzine, isocarboxazid, benzphetamineSsc.28329.1.S1_at DNA polymerase beta 1.14 1.19 1.07 5.25 POLBnelarabine, clofarabine, stavudine, trifluridine, vidarabine,ralcitabine, entecavir Ssc.12202.2.S1_at Farnesyl pyrophosphate 1.12−1.26 −2.68 −1.13 FDPS YM 529, alendronic acid, synthetase pamidronicacid Ssc.19700.1.S1_at Serine/threonine protein 1.11 1.13 1.34 1.09PPP3CB ISAtx-247, tacrolimus, phosphatase 2B catalytic pimecrolimus,cyclosporin A subunit, beta Ssc.8549.1.A1_at Guanylate cyclase soluble,1.11 1.84 −2.00 −2.59 GUCY1A3 nitroglycerin, isosorbide-5- alpha-3 chainmononitrate, isosorbide dinitrate, nitroprusside, isosorbidedinitrate/hydralazine Ssc.15374.1.S1_at COL14A1 protein 1.10 −17.71 3.792.24 COL14A1 collagenase Ssc.15901.1.S1_at cGMP-inhibited 3′,5′-cyclic1.10 −13.33 −3.16 −1.41 PDE3A dyphylline, nitroglycerin,phosphodiesterase A medorinone, aminophylline, cilostazol, dipyridamole,amrinone, tolbutamide, theophylline, pentoxifylline Ssc.16000.1.A1_atVascular endothelial growth 1.08 −3.40 3.34 1.72 FLT1 sunitinib,axitinib, CEP 7055 factor receptor 1 Ssc.20987.1.S1_at Thrombopoietinreceptor 1 1.06 −1.58 −3.97 −5.87 MPL SB-497115 Ssc.11149.1.S1_atCarbonic anhydrase IX 1.04 −1.91 −1.33 −1.26 CA9 cG250, I 131 chimericG250, Y 90 chimeric G250, methazolamide, hydrochlorothiazide,acetazolamide, trichloromethiazide, chlorothiazide, chlorthalidone,benzthiazide, sulfacetamide, topiramate Ssc.8726.1.A1_atAmidophosphoribosyltransferase 1.03 1.24 4.16 −1.11 PPAT6-mercaptopurine, thioguanine, azathioprine Ssc.11406.1.A1_a_atInterleukin-1 receptor, type I 1.03 2.70 −2.44 1.42 IL1R1 anakinraSsc.14506.1.S1_at DNA topoisomerase II, alpha 1.01 3.80 −1.18 −14.30TOP2A novobiocin, etoposide, CPI- 0004Na, pixantrone, becatecarin,elsamitrucin, AQ4N, EN 80927, tafluposide, mitoxantrone, norfloxacin,dexrazoxane, tirapazamine, TAS- 103, gatifloxacin, valrubicin,gemifloxacin, moxifloxacin, nemorubicin, nalidixic acid, epirubicin,doxorubicin, daunorubicin

TABLE 4 Day 21 prescription. Fold Fold Fold Fold Change Change ChangeChange D7/ D21/ D60/ D180/ Gene Probe ID Name Base Base Base Base SymbolDrugs Ssc.23793.1.S1_at T-cell surface antigen CD2 −3.27 79.25 93.345.20 CD2 alefacept, siplizumab SscAffx.20.1.S1_at T-cell surfaceglycoprotein −2.19 14.07 10.96 3.62 CD3G visilizumab, MT103 CD3 gammachain Ssc.19532.1.S1_at Guanylate cyclase soluble, −4.28 12.74 3.04 2.13GUCY1B3 nitroglycerin, isosorbide-5- beta-1 chain mononitrate,isosorbide dinitrate, nitroprusside, isosorbide dinitrate/hydralazineSsc.7176.1.A1_at C—X—C chemokine receptor type 3.74 10.91 8.15 1.68CXCR4 JM 3100 4 (CXC-R4) (CXCR-4) (CD184 antigen). Ssc.2714.1.S1_a_atProto-oncogene tyrosine- −4.26 9.56 12.54 3.93 FYN dasatinib proteinkinase FYN Ssc.15739.1.S1_at Cytokine receptor common −1.12 9.42 1.90−1.28 IL2RG aldesleukin, denileukin gamma chain (Interleukin-2 diftitoxreceptor gamma chain) (IL-2R gamma chain) (CD132 antigen)Ssc.11381.1.S1_at Interferon-alpha/beta receptor 10.45 8.08 2.61 −1.30IFNAR1 interferon beta-1a, interferon alpha chain alfa-2b, interferonalfacon-1, PEG-interferon alfa-2a, interferon alfa-2a/ribavirin,pegintron, interferon beta-1b, IFNA2A Ssc.10256.1.A1_at cAMP-specific3′,5′-cyclic −1.89 6.74 2.20 2.44 PDE4B dyphylline, nitroglycerin,phosphodiesterase 4B arofylline, tetomilast, L 869298, aminophylline,anagrelide, cilomilast, milrinone, rolipram, dipyridamole, L-826,141,roflumilast, tolbutamide, theophylline, pentoxifylline, caffeineSsc.17224.1.S1_at Toll-like receptor 8 1.17 6.49 3.13 −1.52 TLR8resiquimod Ssc.7297.1.S1_at Amine oxidase [flavin- 1.16 6.42 7.02 −1.13NAOB safinamide, ladostigil, containing] B (Monoamine rasagiline,selegiline, oxidase) (MAO-B). dextroamphetamine, procainamide,tranylcypromine, phenelzine, isocarboxazid, benephetamineSsc.15801.1.A1_at Protein kinase C, beta 3.36 6.36 3.53 −4.98 PRKCB1enzastaurin, ruboxistaurin Ssc.20818.1.S1_at Interleukin-2 receptor beta1.43 6.35 −1.17 −5.23 IL2RB humanized MiK-Beta-1, chain (IL-2 receptor)aldesleukin, denileukin diftitox Ssc.12937.1.S1_at Presenilin 1 (PS-1)(S182 −14.09 6.21 2.48 3.79 PSEN1 (R)-flurbiprofen protein).Ssc.15932.1.S1_at Integrin alpha-V −6.15 5.79 2.94 3.14 ITGAV abciximab,CNTO 95, EMD121974 Ssc.26328.1.S1_at C-C chemokine receptor type 5 −2.535.61 3.25 1.29 CCR5 maraviroc, vicriviroc, SCH (CCR5) (CD195 antigen).351125 Ssc.12845.1.S1_at Cell division protein kinase 6 −6.56 5.40 4.775.13 CDK6 PD-0332991, flavopiridol Ssc.17155.1.A1_at heparanase;heparanase-1 4.81 5.38 2.98 −1.83 HPSE heparanase inhibitor PI-88Ssc.13460.1.A1_at Histone deacetylase 9 (HD9) −6.40 5.13 −1.79 5.72HDAC9 tributyrin, PXD101, (HD7B) (HD7) pyroxamide, vorinostat, FR 901228Ssc.24528.1.S1_at Angiotensin-converting enzyme −1.61 5.01 2.33 4.76 ACEpentopril, perindoprilat, amlodipine/benazepril,lisinopril/hydrochlorothiazide, benazepril, enalapril, perindopril,captopril, enalapril/felodipine, hydrochlorothiazide/moexipril,benazepril/hydrochlorothiazide, hydrochlorothiazide/quinapril,fosinopril/hydrochlorothiazide, captopril/hydrochlorothiazide,enalapril/hydrochlorothiazide, ramipril, moexipril, quinapril,lisinopril, enalaprilat, trandolapril, trandolapril/verapamil,diltiazem/enalapril, fosinopril Ssc.26351.1.S1_at cAMP-specific3′,5′-cyclic 4.67 4.99 3.61 −1.15 PDE4D dyphylline, nitroglycerin,phosphodiesterase 4D arofylline, tetomilast, L 869298, aminophylline,anagrelide, cilomilast, milrinone, rolipram, dipyridamole, L-826,141,roflumilast, tolbutamide, theophylline, pentoxifylline, caffeineSsc.15601.1.A1_s_at Interleukin-1 beta precursor, 8.18 4.65 −14.71 −2.84IL1B IL-1 trap (IL-1 beta) Ssc.3607.1.S1_at Interferon-alpha/betareceptor 2.28 4.65 1.11 −1.56 IFNAR2 interferon beta-1a, interferon betachain alfa-2b, interferon alfacon-1, PEG-interferon alfa-2a, interferonalfa-2a/ribavirin, pegintron, interferon beta-1b, IFNA2ASsc.20841.1.S1_at Proto-oncogene tyrosine- −1.13 4.37 −2.59 −1.93 SRCdasatinib, AZM-475271 protein kinase Src Ssc.11200.1.S1_a_atProto-oncogene tyrosine- −1.15 4.28 −3.41 −1.18 ABL1 imatinib,temozolomide protein kinase ABL1 Ssc.22974.1.A1_at Metabotropicglutamate −1.05 4.28 −2.05 −5.66 GRM1 fasoracetam receptor 1Ssc.7111.1.A1_at Ribonucleoside-diphosphate −13.13 4.08 1.37 1.67 RRM2gemcitabine, triapine, reductase M2 chain hydroxyurea, fludarabine(Ribonucleotide reductase phosphate small chain) Ssc.9272.1.S1_atTumor-associated calcium 1.81 3.94 176.50 2.07 TACSTD1 tucotuzumabcelmoleukin signal transducer 1 (EPCAM antigen) Ssc.16160.1.S1_at Tlymphocyte activation −1.55 3.88 −1.37 1.18 CD86 abatacept antigen CD86Ssc.14506.1.S1_at DNA topoisomerase II, alpha 1.01 3.80 −1.18 −14.30TOP2A novobiocin, etoposide, CPI- isozyme 0004Na, pixantrone,becatecarin, elsamitrucin, AQ4N, BN 80927, tafluposide, mitoxantrone,norfloxacin, dexrazoxane, tirapazamine, TAS- 103, gatifloxacin,valrubicin, gemifloxacin, moxifloxacin, nemorubicin, nalidixic acid,epirubicin, doxorubicin, daunorubicin Ssc.15822.1.S1_at Coagulationfactor V 1.92 3.76 1.89 −1.75 F5 drotrecogin alfa (Activated protein Ccofactor). Ssc.9034.1.A1_at Proteinase activated receptor −1.29 3.75−1.40 1.37 F2R chrysalin, argatroban, 1 precursor (PAR-1) (Thrombinbivalirudin receptor) Ssc.15886.1.S1_at Apopain precursor (Caspase-3)−3.02 3.64 2.31 2.29 CASP3 IDN-6556 (CASP-3) Ssc.17518.1.S1_at AdenosineA1 receptor −3.16 3.44 −1.56 1.58 ADORA1 adenosine, dyphylline,aminophylline, clofarabine, theophylline, caffeine, tecadenosonSsc.14258.1.S1_at Amyloid beta A4 protein 1.87 3.33 1.34 −1.02 APPAAB-001 precursor (APP) (ABPP) Ssc.14471.1.S1_at B-lymphocyte antigenCD19 9.54 3.30 −10.32 3.04 CD19 combotox, HD37-dgRTA, MT103 precursor(Differentiation antigen CD19 Ssc.15878.1.S1_at Serine/threonine protein1.85 3.22 3.62 −1.49 PPP3CA ISAtx-247, tacrolimus, phosphatase 2Bcatalytic pimecrolimus, cyclosporin A subunit, alpha Ssc.21108.1.S1_atComplement C5 −17.35 3.21 618.80 9.28 C5 eculizumab Ssc.16186.1.S1_atT-cell surface glycoprotein 9.00 3.12 2.12 −5.66 CD3E visilizumab,MT103, muromonab- CD3 epsilon chain (T-cell CD3 surface antigen T3/Leu-4epsilon chain) Ssc.24966.1.S1_at Purine nucleoside −3.34 3.12 3.46 −1.14NP forodesine, 9-deaza-9-(3- phosphorylase (Inosinethienylmethyl)guanine phosphorylase) (PNP). Ssc.19873.1.S1_at Collagenalpha 1(XVII) chain −2.37 3.02 −1.55 2.18 COL17A1 collagenase (Bullouspemphigoid antigen 2) Ssc.20904.1.A1_at RAC-gamma serine/threonine-−1.34 3.01 −2.18 1.23 AKT3 enzastaurin protein kinase (RAC-PK-gamma)(Protein kinase Akt-3) (Protein kinase B, gamma) (PKB gamma) (STK-2)Ssc.26646.1.S1_at Glutamate receptor 1 −1.10 2.91 −5.42 −3.43 GRIA1talampanel, Org 24448, LY451395, tezampanel Ssc.15312.1.S1_at Histonedeacetylase 4 (HD4) −1.93 2.85 −2.41 1.20 HDAC4 tributyrin, PXD101,pyroxamide, vorinostat, FR 901228 Ssc.24889.1.S1_at Arachidonate12-lipoxygenase, 1.97 2.83 −1.18 −2.78 ALOX12 sulfasalazine,balsalazide, 5- 12S-type aminosalicylic acid, masoprocol, verteportinSsc.12630.1.A1_at Sodium/potassium-transporting 2.97 2.81 −7.30 −2.03ATP1A1 digoxin, omeprazole, ATPase alpha-1 chain ethacrynic acid,perphenazine Ssc.3040.1.S1_at Histone deacetylase 2 (HD2) −3.24 2.794.94 4.72 HDAC2 tributyrin, PXD101, pyroxamide, vorinostat, FR901228Ssc.12791.1.A1_at 3-hydroxy-3-methylglutaryl- 3.27 2.77 1.77 −2.56 HMGCRaspirin/pravastatin, coenzyme A reductase (HMG-CoA lovastatin/niacin,reductase) ezetimibe/simvastatin, amlodipine/atorvastatin, fluvastatin,cerivastatin, atorvastatin, pravastatin, simvastatin, lovastatin,rosuvastatin Ssc.20685.1.S1_at Apoptosis regulator Bcl-2 −2.22 2.77 2.583.25 BCL2 oblimersen, (−)-gossypol Ssc.15965.1.S1_at Inward rectifierpotassium 4.68 2.72 −1.84 −4.62 KCNJ2 nicorandil, amiodarone channel 2(Potassium channel, inwardly rectifying, subfamily J, member 2) (Inwardrectifier K+ channel Kir2.1) (Cardiac inward rectifier potassiumchannel) (IRK1). Ssc.19673.1.S1_at T-cell surface glycoprotein 6.40 2.702.03 −11.77 CD3D visilizumab, MT103 CD3 delta chain precursor (T- cellreceptor T3 delta chain) Ssc.16127.1.S1_at Adrenocorticotropic hormone−1.67 2.70 −2.51 −1.10 MC2R cosyntropin, ACTH receptor (ACTH receptor)(ACTH-R) Ssc.11406.1.A1_a_at Interleukin-1 receptor, type I 1.03 2.70−2.44 1.42 IL1R1 anakinra precursor (IL-1R-1) (IL-1R- alpha) (P80)(Antigen CD121a) Ssc.19937.1.S1_at Inosine-5′-monophosphate 1.00 2.69−1.47 3.65 IMPDH2 thioguanine, VX-944, dehydrogenase 2 (IMP interferonalfa-2a/ribavirin, dehydrogenase 2) mycophenolic acid, ribavirinSsc.818.1.S1_at RAF proto-oncogene −1.40 2.56 1.58 1.98 RAF1 sorafenibserine/threonine-protein kinase Ssc.14129.1.A1_at 4-aminobutyrate 6.912.56 −21.17 −3.35 ABAT valproic acid aminotransferase, mitochondrialprecursor (Gamma-amino-N-butyrate transaminase) (GABA transaminase)Ssc.13186.1.S1_at Cell division protein kinase 7 −1.08 2.38 4.34 1.24CDK7 BMS-387032, flavopiridol Ssc.16167.1.S1_at Rho-associated proteinkinase 1 2.40 2.32 2.83 3.00 ROCK1 fasudil, Y-27632 Ssc.6418.1.S1_atFarnesyl-diphosphate −1.25 2.31 1.33 1.08 FDFT1 TAK-475, zoledronic acidfarnesyltransferase Ssc.15829.1.S1_at Retinoic acid receptor alpha −1.732.23 −1.33 −1.16 RARA etretinate, adapalene, arsenic trioxide,13-cis-retinoic acid, tazarotene, acitretin, retinoic acid,9-cis-retinoic acid Ssc.10142.1.A1_at Dihydropyrimidine 2.06 2.17 1.13−2.68 DPYD eniluracil dehydrogenase [NADP+] (DPD) (DHPDHase)(Dihydrouracil dehydrogenase) (Dihydrothymine dehydrogenase).Ssc.23505.1.S1_at Amine oxidase [flavin- −1.86 2.17 1.08 1.20 MAOAladostigil, 1- containing] A (Monoamine ethylphenoxathiin 10,10-oxidase) (MAO-A) dioxide, dextroamphetamine, procainamide,tranylcypromine, phenelzine, isocarboxazid, benzphetamine, N-(2-indanyl)glycinamide Ssc.20438.1.S1_at Prostaglandin F2-alpha −3.20 2.135.28 −38.97 PTGFR tafluprost, travoprost, receptor (Prostanoid FPisopropyl unoprostone, receptor) (PGF receptor) (PGF2 bimatoprost,latanoprost alpha receptor). Ssc.4756.1.A1_at Adenosine A3 receptor 2.152.10 1.88 −1.81 ADORA3 adenosine, dyphylline, aminophylline,clofarabine, theophylline, caffeine Ssc.11302.1.S1_at Collagen alpha1(III) chain −1.80 2.02 2.06 1.26 COL3A1 collagenase Ssc.19400.2.A1_atPresenilin 2 (PS-2) (STM-2) −2.32 1.99 −5.30 −3.44 PSEN2(R)-flurbiprofen (E5-1) (AD3LP) (AD5) Ssc.3059.1.S1_at Aldose reductase(AR) −1.74 1.98 −1.66 2.49 AKR1B1 sorbinil, Zopolrestat (Alond,(Aldehyde reductase). Pfizer), zenarestat (Fujisawa, Parke-Davis)Ssc.18051.1.S1_at cGMP-inhibited 3′,5′-cyclic −3.16 1.96 3.41 2.32 PDE3Bdyphylline, nitroglycerin, phosphodiesterase B (Cyclic medorinone,aminophylline, GMP inhibited cilostazol, dipyridamole, phosphodiesteraseB) (CGI-PDE amrinone, tolbutamide, B) (CGIPDE1) (CGIP1) theophylline,pentoxifylline Ssc.2548.1.S1_at DNA polymerase epsilon p17 2.27 1.93−1.67 −1.21 POLE3 gemcitabine subunit (DNA polymerase epsilon subunit 3)(Chromatin accessibility complex 17) (HuCHRAC17) (CHRAC-17).Ssc.11383.1.A1_at Glutamate receptor 3 precursor 2.61 1.85 −1.87 −2.43GRIA3 talampanel, Org 24448, (GluR-3) (GluR-C) (GluR-K3) LY451395,tezampanel (Glutamate receptor ionotropic, AMPA 3) Ssc.8549.1.A1_atGuanylate cyclase soluble, 1.11 1.84 −2.00 −2.59 GUCY1A3 nitroglycerin,isosorbide-5- alpha-3 chain (GCS-alpha-3) mononitrate, isosorbide(Soluble guanylate cyclase dinitrate, nitroprusside, large subunit)(GCS-alpha-1). isosorbide dinitrate/hydralazine Ssc.12781.1.A1_atToll-like receptor 4 2.39 1.83 −1.52 −6.10 TLR4 TAK-242 Ssc.6301.1.S1_atAromatic-L-amino-acid 1.76 1.80 −4.91 −1.88 DDCcarbidopa/entacapone/levodopa, decarboxylase (AADC) (DOPAcarbidopa/levodopa, S(−)- decarboxylase) carbidopa, L-dopaSsc.6801.1.S1_at Proto-oncogene tyrosine- −1.06 1.69 2.36 −1.82 YES1dasatinib protein kinase YES Ssc.5371.1.S1_a_at DNA polymerase epsilonsubunit 10.16 1.68 −1.37 −3.14 POLE2 gemcitabine B (DNA polymerase IIsubunit B). Ssc.11572.1.A1_at Histone deacetylase 3 (HD3) −1.65 1.67−1.55 2.36 HDAC3 tributyrin, PXD101, (RPD3-2) (SMAP45) pyroxamide,MGCD0103, vorinostat, FR 901228 Ssc.23234.1.S1_at collagen, type XXIV,alpha 1 −1.43 1.66 1.16 1.76 COL24A1 collagenase Ssc.9565.1.S1_atInterferon-gamma receptor 2.92 1.63 1.41 −1.23 IFNGR1 interferongamma-1b alpha chain precursor (IFN- gamma-R1) (CD119 antigen)Ssc.5021.1.S1_at Glutamate decarboxylase, 65 kDa −29.44 1.62 −10.79−5.61 GAD2 valproic acid isoform (GAD-65) (65 kDa glutamic aciddecarboxylase) Ssc.14326.1.A1_at Mitogen-activated protein 12.63 1.56−1.80 −7.24 MAPK13 SCIO-469 kinase 13 (Stress-activated proteinkinase-4) (Mitogen- activated protein kinase p38 delta) (MAP kinase p38delta) Ssc.10591.1.A1_at Metabotropic glutamate −7.83 1.54 −1.31 1.40GRM5 fasoracetam receptor 5 precursor (mGluR5) Ssc.30373.1.A1_atcGMP-specific 3′,5′-cyclic 4.27 1.52 2.34 4.09 PDE5A dyphylline,nitroglycerin, DA- phosphodiesterase 8159, aminophylline, sildenafil,dipyridamole, aspirin/dipyridamole, vardenafil, tolbutamide, tadalafil,theophylline, pentoxifylline Ssc.6710.1.A1_at Ribonucleoside-diphosphate−1.90 1.44 2.01 −1.01 RRM1 gemcitabine, clofarabine, reductase M1 chainfludarabine phosphate (Ribonucleotide reductase large chain)Ssc.7139.1.S1_at Dihydrofolate reductase −1.13 1.41 −1.12 2.06 DHFRpyrimethamine, trimethoprim, iclaprim, methotrexate, sulfisoxazole,triamterene, folic acid, trimetrexate, LY231514, PT 523 Ssc.5538.1.S1_atCarbonic anhydrase II 8.09 1.39 −2.25 −1.35 CA2 methazolamide,(Carbonate dehydratase II) hydrochlorothiazide, (CA-II) (Carbonicanhydrase C) acetazolamide, trichloromethiazide, dorzolamide,chlorothiazide, dorzolamide/timolol, brinzolamide, chlorthalidone,benzthiazide, sulfacetamide, topiramate Ssc.5569.1.S1_at Thyroid hormonereceptor alpha −10.22 1.26 1.26 6.49 THRA 3,5-diiodothyropropionic acid,(C-erbA-alpha) (c-erbA-1) amiodarone, thyroxine, L- (EAR-7) (EAR7)triiodothyronine Ssc.10360.1.S1_at B-Raf proto-oncogene −2.15 1.26 3.091.36 BRAF sorafenib serine/threonine-protein kinase Ssc.19672.1.S1_atRAC-alpha serine/threonine- 17.77 1.25 −19.82 −2.11 AKT1 enzastaurinprotein kinase (RAC-PK-alpha) (Protein kinase B) (PKB) (C- AKT)Ssc.21011.1.S1_at Collagen alpha 2(I) chain −2.70 1.24 3.12 −1.01 COL1A2collagenase Ssc.5045.1.S1_at 3-beta-hydroxysteroid- −1.55 1.24 2.19 2.08EBP SR 31747 delta(8),delta(7)-isomerase (Cholestenol delta-isomerase)(Delta8-delta7 sterol isomerase) (D8-D7 sterol isomerase)(Emopamil-binding protein) Ssc.8726.1.A1_atAmidophosphoribosyltransferase 1.03 1.24 4.16 −1.11 PPAT6-mercaptopurine, thioguanine, precursor (Glutamine azathioprinephosphoribosylpyrophosphate amidotransferase) (ATASE) (GPAT)Ssc.10219.1.A1_at Excitatory amino acid 1.36 1.24 −3.38 −1.03 SLC1A6riluzole transporter 4 (Sodium- dependent glutamate/aspartatetransporter) Ssc.15999.1.A1_at Vascular endothelial growth 1.24 1.2418.52 −11.02 KDR AEE 788, sunitinib, AZD 2171, factor receptor 2precursor pazopanib, XL647, CEP 7055, (VEGFR-2) (Kinase insertBMS-582664, KRN-951, vatalanib, domain receptor) (Protein- sorafenib,vandetanib, tyrosine kinase receptor Flk- pegaptanib 1) Ssc.9348.1.S1_atPeroxisome proliferator −1.05 1.22 −3.05 −1.52 PPARA NS-220,tesaglitazar, activated receptor alpha clofibrate, fenofibrate,(PPAR-alpha) docosahexaenoic acid, gemfibrozil Ssc.1498.1.S1_atProteasome subunit beta type 5 −1.81 1.19 1.38 5.94 PSMB5 bortezomibprecursor (Proteasome epsilon chain) (Macropain epsilon chain)(Multicatalytic endopeptidase complex epsilon chain) (Proteasome subunitX) (Proteasome chain 6) (Proteasome subunit MB1) Ssc.6934.1.A1_atThymidylate synthase (EC −1.13 1.19 −1.11 −2.81 TYMS flucytosine,5-fluorouracil, 2.1.1.45) (TS) (TSase) (OK/SW- plevitrexed, nolatrexed,c1.29) capecitabine, trifluridine, floxuridine, LY231514Ssc.28329.1.S1_at DNA polymerase beta 1.14 1.19 1.07 5.25 PCLBnelarabine, clofarabine, stavudine, trifluridine, vidarabine,zalcitabine, entecavir Ssc.16823.1.S1_at P2Y purinoceptor 12 (P2Y12)1.38 1.19 1.41 1.11 P2RY12 prasugrel, AZD 6140 (P2Y12 platelet ADPreceptor) (Ticagrelor), clopidogrel (P2Y(ADP)) (ADP-glucose receptor)(ADPG-R) (P2Y(AC)) (P2Y(cyc)) (P2T(AC)) (SP1999 Ssc.19691.1.S1_atPlatelet-activating factor 1.59 1.16 3.01 1.47 PLA2G7 darapladibacetylhydrolase precursor (EC 3.1.1.47) (PAF acetylhydrolase) (PAF 2-acylhydrolase) (LDL-associated phospholipase A2) (LDL-PLA(2))(2-acetyl-1- alkylglycerophosphocholine esterase) (1-alkyl-2-acetylglycerophosphocholine esterase) Ssc.15880.1.S1_at Cysteinylleukotriene receptor 2.86 1.14 −2.12 −3.42 CYSLTR2 montelukast,zafirlukast 2 (CysLTR2) (PSEC0146) (HG57) (HPN321) (hGPCR21)Ssc.11147.1.S1_at Aldehyde dehydrogenase, 3.18 1.13 2.00 −1.68 ALDH2disulfiram, chlorpropamide mitochondrial precursor (EC 1.2.1.3) (ALDHclass 2) (ALDHI) (ALDH-E2) Ssc.1908.1.S1_at FKBP-rapamycin associated1.99 1.13 −1.88 −1.46 FRAP1 AP23573, temsirolimus, protein (FRAP)(Rapamycin tacrolimus, everolimus target protein) Ssc.19700.1.S1_atSerine/threonine protein 1.11 1.13 1.34 1.09 PPP3CB ISAtx-247,tacrolimus, phosphatase 2B catalytic pimecrolimus, cyclosporin Asubunit, beta Ssc.30147.1.A1_at Fibroblast growth factor 1.56 1.13 −1.05−1.18 FGFR2 palifermin receptor 2 precursor (FGFR-2) (Keratinocytegrowth factor receptor 2) Ssc.27232.1.S1_at Succinate semialdehyde 2.061.12 −2.84 −5.73 ALDH5A1 valproic acid dehydrogenase, mitochondrialprecursor (NAD(+)-dependent succinic semialdehyde dehydrogenase)Ssc.10215.1.A1_at High-affinity cAMP-specific 1.83 1.12 −8.48 −15.51PDE8A dyphylline, nitroglycerin, and IBMX-insensitive 3′,5′-aminophylline, anagrelide, cyclic phosphodiesterase 8A milrinone,dipyridamole, tolbutamide, theophylline, pentoxifyllineSsc.2767.2.S1_a_at Prostaglandin E2 receptor, EP3 2.30 1.12 −1.59 −6.78PTGER3 prostaglandin E1 subtype (Prostanoid EP3 receptor) (PGE receptor,EP3 subtype) Ssc.15955.1.S1_at Antithrombin-III precursor −1.89 1.12−2.06 −2.42 SERPINC1 enoxaparin, SR-123781A, (ATIII) (PRO0309)fondaparinux Ssc.25040.1.S1_at Serine/threonine-protein −3.75 1.11 1.06−2.45 CHEK1 UCN-01 (7- kinase Chk1 hydroxystaurosporine)Ssc.14488.1.S1_at Glutamate carboxypeptidase II −1.04 1.10 1.02 1.69FOLH1 capromab pendetide (Membrane glutamate carboxypeptidase)Ssc.1.1.S1_at 3-oxo-5-alpha-steroid 4- −1.77 1.05 −4.11 −1.09 SRD5A2finasteride, dutasteride dehydrogenase 2 (Steroid 5- alpha-reductase 2)(SR type 2) (5 alpha-SR2) Ssc.7581.1.A1_at FL cytokine receptorprecursor 1.69 1.04 −1.81 1.01 FLT3 CHIR-258, sorafenib,(Tyrosine-protein kinase lestaurtinib, CGP 41251 receptor FLT3) (Stemcell tyrosine kinase 1) (STK-1) (CD135 antigen)

TABLE 5 Day 60 prescription. Fold Fold Fold Fold Change Change ChangeChange D7/ D21/ D60/ D180/ Gene Probe ID Name Base Base Base Base SymbolDRUGS Ssc.21108.1.S1_at Complement C5 −17.35 3.21 618.80 9.28 C5eculizumab Ssc.9272.1.S1_at Tumor-associated calcium 1.81 3.94 176.502.07 TACSTD1 tucotuzumab celmoleukin signal transducer 1 (EPCAM antigen)Ssc.23793.1.S1_at T-cell surface antigen CD2 −3.27 79.25 93.34 5.20 CD2alefacept, siplizumab Ssc.17245.1.S1_at Interleukin-13 receptor alpha-−1.99 23.04 21.92 7.16 IL13RA1 cintredekin besudotox 1 chainSsc.15999.1.A1_at Vascular endothelial growth 1.24 1.24 18.52 −11.02 KDRAEE 788, sunitinib, AZD 2171, factor receptor 2 pazopanib, XL647, CEP7055, BMS- 582664, KRN-951, vatalanib, sorafenib, vandetanib, pegaptanibSsc.27603.1.S1_at Endothelin B receptor 5.30 −3.27 15.99 1.23 EDNRBbosentan, sitaxsentan, precursor (ET-B) (Endothelin atrasentan receptorNon-selective type) Ssc.2714.1.S1_a_at Proto-oncogene tyrosine- −4.269.56 12.54 3.93 FYN dasatinib protein kinase FYN SscAffx.20.1.S1_atT-cell surface glycoprotein −2.19 14.07 10.96 3.62 CD3G visilizumab,MT103 CD3 gamma chain Ssc.7176.1.A1_at C—X—C chemokine receptor type3.74 10.91 8.15 1.68 CXCR4 JM 3100 4 (CXC-R4) (CXCR-4) Ssc.26200.1.S1_atThyroid hormone receptor beta-1 3.49 −1.56 7.96 2.52 THRB3,5-diiodothyropropionic acid, amiodarone, thyroxine, L-triiodothyronine Ssc.7297.1.S1_at Amine oxidase [flavin- 1.16 6.42 7.02−1.13 MAOB safinamide, ladostigil, containing] B(Monoamine rasagiline,selegiline, oxidase) (MAO-B). dextroamphetamine, procainamide,tranylcypromine, phenelzine, isocarboxazid, benzphetamineSsc.9019.1.A1_at Atrial natriuretic peptide −1.09 −1.69 5.31 1.18 NPR3nesiritide clearance receptor precursor (ANP-C) (ANPRC)Ssc.20438.1.S1_at Prostaglandin F2-alpha −3.20 2.13 5.28 −38.97 PTGFRtafluprost, travoprost, receptor isopropyl unoprostone, bimatoprost,latanoprost Ssc.3040.1.S1_at Histone deacetylase 2 (HD2) −3.24 2.79 4.944.72 HDAC2 tributyrin, PXD101, pyroxamide, vorinostat, FR 901228Ssc.26325.1.S1_at Cystic fibrosis transmembrane 1.60 −5.71 4.77 −8.99CFTR SP 303 conductance regulator (CFTR) Ssc.12845.1.S1_at Cell divisionprotein kinase 6 −6.56 5.40 4.77 5.13 CDK6 PD-0332991, flavopiridolSsc.13186.1.S1_at Cell division protein kinase 7 −1.08 2.38 4.34 1.24CDK7 BMS-387032, flavopiridol Ssc.8726.1.A1_atAmidophosphoribosyltransferase 1.03 1.24 4.16 −1.11 PPAT6-mercaptopurine, thioguanine, azathioprine Ssc.15374.1.S1_at COL14A1protein 1.10 −17.71 3.79 2.24 COL14A1 collagenase Ssc.1147.1.A1_atLipoprotein lipase 4.05 −5.49 3.78 −8.08 LPL nicotinic acid,lovastatin/niacin Ssc.15878.1.S1_at Serine/threonine protein 1.85 3.223.62 −1.49 PPP3CA ISAtx-247, tacrolimus, phosphatase 2B catalyticpimecrolimus, cyclosporin A subunit, alpha Ssc.26351.1.S1_atcAMP-specific 3′,5′-cyclic 4.67 4.99 3.61 −1.15 PDE4D dyphylline,nitroglycerin, phosphodiesterase 4D arofylline, tetomilast, L 869298,aminophylline, anagrelide, cilomilast, milrinone, rolipram,dipyridamole, L-826,141, roflumilast, tolbutamide, theophylline,pentoxifylline, caffeine Ssc.15801.1.A1_at Protein kinase C, beta 3.366.36 3.53 −4.98 PRKCB1 enzastaurin, ruboxistaurin Ssc.10055.1.A1_atAlpha platelet-derived growth −2.14 −1.46 3.52 −1.14 PDGFRA sunitinib,axitinib, imatinib, factor receptor becaplermin Ssc.24966.1.S1_at Purinenucleoside −3.34 3.12 3.46 −1.14 NP forodesine, 9-deaza-9-(3-phosphorylase thienylmethyl)guanine Ssc.18051.1.S1_at cGMP-inhibited3′,5′-cyclic −3.16 1.96 3.41 2.32 PDE3B dyphylline, nitroglycerin,phosphodiesterase B medorinone, aminophylline, cilostazol, dipyridamole,amrinone, tolbutamide, theophylline, pentoxifylline Ssc.9523.1.A1_atMethylated-DNA--protein- 1.55 −1.17 3.35 1.47 MGMT O6-benzylguaninecysteine methyltransferase Ssc.16000.1.A1_at Vascular endothelial growth1.08 −3.40 3.34 1.72 FLT1 sunitinib, axitinib, CEP 7055 factor receptor1 Ssc.26328.1.S1_at C-C chemokine receptor type 5 −2.53 5.61 3.25 1.29CCR5 maraviroc, vicriviroc, SCH (CCR5) (CD195 antigen). 351125Ssc.17224.1.S1_at Toll-like receptor 8 1.17 6.49 3.13 −1.52 TLR8resiquimod Ssc.21011.1.S1_at Collagen alpha 2(I) chain −2.70 1.24 3.12−1.01 COL1A2 collagenase Ssc.10360.1.S1_at B-Raf proto-oncogene −2.151.26 3.09 1.36 BRAF sorafenib serine/threonine-protein kinaseSsc.19532.1.S1_at Guanylate cyclase soluble, −4.28 12.74 3.04 2.13GUCY1B3 nitroglycerin, isosorbide-5- beta-1 chain mononitrate,isosorbide dinitrate, nitroprusside, isosorbide dinitrate/hydralazineSsc.19691.1.S1_at Platelet-activating factor 1.59 1.16 3.01 1.47 PLA2G7darapladib acetylhydrolase precursor Ssc.17155.1.A1_at heparanase;heparanase-1 4.81 5.38 2.98 −1.83 HPSE heparanase inhibitor PI-88Ssc.15932.1.S1_at Integrin alpha-V precursor −6.15 5.79 2.94 3.14 ITGAVabciximab, CNTO 95, EMD121974 Ssc.16167.1.S1_at Rho-associated proteinkinase 1 2.40 2.32 2.83 3.00 ROCK1 fasudil, Y-27632 Ssc.62.2.S1_a_atInterleukin-6 (IL-6) 1.89 −6.32 2.77 −1.04 IL6 tocilizumabSsc.11246.1.A1_at Protein kinase C, alpha −5.96 −4.78 2.68 2.46 PRKCAL-threo-safingol Ssc.11381.1.S1_at Interferon-alpha/beta receptor 10.458.08 2.61 −1.30 IFNAR1 interferon beta-1a, interferon alpha alfa-2b,interferon alfacon-1, PEG-interferon alfa-2a, interferonalfa-2a/ribavirin, pegintron, interferon beta-1b, IFNA2ASsc.20685.1.S1_at Apoptosis regulator Bcl-2 −2.22 2.77 2.58 3.25 BCL2oblimersen, (—)-gossypol Ssc.12937.1.S1_at Presenilin 1 (PS-1) (S182−14.09 6.21 2.48 3.79 PSEN1 (R)-flurbiprofen protein) Ssc.8500.1.A1_atGlutamate receptor 4 precursor −1.04 −1.13 2.39 −7.80 GRIA4 talampanel,Org 24448, LY451395, (GluR-4) (GluR4) (GluR-D) tezampanel (Glutamatereceptor ionotropic, AMPA 4) Ssc.6801.1.S1_at Proto-oncogene tyrosine-−1.06 1.69 2.36 −1.82 YES1 dasatinib protein kinase YESSsc.30373.1.A1_at cGMP-specific 3′,5′-cyclic 4.27 1.52 2.34 4.09 PDE5Adyphylline, nitroglycerin, DA- phosphodiesterase 8159, aminophylline,sildenafil, dipyridamole, aspirin/dipyridamole, vardenafil, tolbutamide,tadalafil, theophylline, pentoxifylline Ssc.15886.1.S1_at Apopainprecursor (Caspase-3) −3.02 3.64 2.31 2.29 CASP3 IDN-6556 (CASP-3)Ssc.16114.1.S1_at Dihydropyridine-sensitive L- −1.96 −4.18 2.24 3.65CACNA2D1 bepridil, amlodipine, pregabalin type, calcium channel alpha-2/delta subunits Ssc.10256.1.A1_at cAMP-specific 3′,5′-cyclic −1.89 6.742.20 2.44 PDE4B dyphylline, nitroglycerin, phosphodiesterase 4B (ECarofylline, tetomilast, L 869298, 3.1.4.17) (DPDE4) (PDE32)aminophylline, anagrelide, cilomilast, milrinone, rolipram,dipyridamole, L-826,141, roflumilast, tolbutamide, theophylline,pentoxifylline, caffeine Ssc.5045.1.S1_at 3-beta-hydroxysteroid- −1.551.24 2.19 2.08 EBP SR 31747 delta(8), delta(7)-isomerase(Emopamil-binding protein) Ssc.204.1.S1_at Cytochrome P450 3A4 1.97−3.35 2.16 −1.42 CYP3A4 ketoconazole Ssc.16186.1.S1_at T-cell surfaceglycoprotein 9.00 3.12 2.12 −5.66 CD3E visilizumab, MT103, muromonab-CD3 epsilon chain CD3 Ssc.1091.1.S1_at Collagen alpha 1(I) chain −3.27−17.59 2.07 1.03 COL1A1 collagenase Ssc.11302.1.S1_at Collagen alpha1(III) chain −1.80 2.02 2.06 1.26 COL3A1 collagenase Ssc.19673.1.S1_atT-cell surface glycoprotein 6.40 2.70 2.03 −11.77 CD3D visilizumab,MT103 CD3 delta chain Ssc.6710.1.A1_at Ribonucleoside-diphosphate −1.901.44 2.01 −1.01 RRM1 gemcitabine, clofarabine, reductase M1 chainfludarabine phosphate (Ribonucleotide reductase large chain)Ssc.11147.1.S1_at Aldehyde dehydrogenase, 3.18 1.13 2.00 −1.68 ALDH2disulfiram, chlorpropamide mitochondrial precursor ((ALDHI)Ssc.1520.1.A1_at Proto-oncogene tyrosine- −1.05 −1.88 2.00 2.39 RETsunitinib protein kinase receptor ret Ssc.30888.1.S1_atVoltage-dependent L-type 2.92 −2.72 1.90 −7.82 CACNA1D MEM-1003,mibefradil, bepridil, calcium channel alpha-1D nisoldipine, isradipine,subunit nicardipine Ssc.15739.1.S1_at Cytokine receptor common gamma−1.12 9.42 1.90 −1.28 IL2RG aldesleukin, denileukin diftitox chain(IL-2R gamma chain) CD132 antigen) Ssc.15822.1.S1_at Coagulation factorV 1.92 3.76 1.89 −1.75 F5 drotrecogin alfa (Activated protein Ccofactor) Ssc.4756.1.A1_at Adenosine A3 receptor. 2.15 2.10 1.88 −1.81ADORA3 adenosine, dyphylline, aminophylline, clofarabine, theophylline,caffeine Ssc.12791.1.A1_at 3-hydroxy-3-methylglutaryl- 3.27 2.77 1.77−2.56 HMGCR aspirin/pravastatin, coenzyme A reductase (HMG-CoAlovastatin/niacin, reductase) ezetimibe/simvastatin,amlodipine/atorvastatin, fluvastatin, cerivastatin, atorvastatin,pravastatin, simvastatin, lovastatin, rosuvastatin Ssc.27293.1.A1_atHypoxanthine-guanine 2.15 −1.16 1.63 −7.14 HPRT1 6-mercaptopurine,thioguanine, phosphoribosyltransferase azathioprine (HGPRT)Ssc.16189.1.S1_at Endothelin-1 receptor −1.11 −2.54 1.58 −2.91 EDNRAbosentan, avosentan, (Endothelin A receptor) (ET-A) clazosentan,ambrisentan, sitaxsentan, ZD4054, SB 234551, TBC 3214, BSF 302146, PD180988, atrasentan Ssc.818.1.S1_at RAF proto-oncogene −1.40 2.56 1.581.98 RAF1 sorafenib serine/threonine-protein kinase Ssc.15748.2.S2_at Tlymphocyte activation 1.95 −1.24 1.54 −3.12 CD80 abatacept antigen CD80Ssc.19059.1.A1_at Type-1 angiotensin II receptor 5.57 −2.57 1.50 −11.08AGTR1 amlodipine/olmesartan medoxomil, (AT1) (AT1AR)losartan/hydrochlorothiazide, valsartan/hydrochlorothiazide, candesartancilexetil, olmesartan medoxomil, irbesartan, losartan potassium,telmisartan, eprosartan, candesartan cilexetil/hydrochlorothiazide,hydrochlorothiazide/irbesartan, eprosartan/hydrochlorothiazide,hydrochlorothiazide/telmisartan, hydrochlorothiazide/olmesartanmedoxomil, valsartan Ssc.18459.1.S1_at Amiloride-sensitive sodium 1.97−2.41 1.43 −1.93 SCNN1A triamterene/hydrochlorothiazide, channelalpha-subunit amiloride, amiloride/hydrochlorothiazide, triamtereneSsc.10287.1.A1_at Transforming growth factor 1.41 −4.54 1.43 1.67 TGFB2AP-12009 beta 2 precursor (TGF-beta 2) Ssc.16823.1.S1_at P2Ypurinoceptor 12 (P2Y12) 1.38 1.19 1.41 1.11 P2RY12 prasugrel, AZD 6140,clopidogrel (P2Y12 platelet ADP receptor) (P2Y(ADP)) Ssc.9565.1.S1_atInterferon-gamma receptor 2.92 1.63 1.41 −1.23 IFNGR1 interferongamma-1b alpha chain Ssc.9595.1.S1_at Beta platelet-derived growth 3.48−3.60 1.40 1.65 PDGFRB dasatinib, sunitinib, axitinib, factor receptorKRN-951, imatinib, sorafenib, becaplermin Ssc.8046.1.A1_atpeptidylprolyl isomerase A 1.16 −1.08 1.39 1.26 PPIAN-methyl-4-Ile-cyclosporin isoform 1; cyclophilin A; Ssc.1498.1.S1_atProteasome subunit beta type 5 −1.81 1.19 1.38 5.94 PSMB5 bortezomibSsc.7111.1.A1_at Ribonucleoside-diphosphate −13.13 4.08 1.37 1.67 RRM2gemcitabine, triapine, reductase M2 chain hydroxyurea, fludarabine(Ribonucleotide reductase phosphate small chain) Ssc.19700.1.S1_atSerine/threonine protein 1.11 1.13 1.34 1.09 PPP3CB ISAtx-247,tacrolimus, phosphatase 2B catalytic pimecrolimus, cyclosporin Asubunit, beta Ssc.14258.1.S1_at Amyloid beta A4 protein 1.87 3.33 1.34−1.02 APP AAB-001 precursor (APP) (ABPP) Ssc.6418.1.S1_atFarnesyl-diphosphate −1.25 2.31 1.33 1.08 FDFT1 TAK-475, zoledronic acidfarnesyltransferase Ssc.16096.2.S1_a_at Mast/stem cell growth factor−1.28 −2.63 1.30 −4.71 KIT dasatinib, sunitinib, KRN-951, receptorimatinib, sorafenib Ssc.29149.1.A1_at Mineralocorticoid receptor −2.18−2.78 1.28 −11.66 NR3C2 hydrochlorothiazide/spironolactone, (MR)fludrocortisone acetate, drospirenone, spironolactone, eplerenoneSsc.5569.1.S1_at Thyroid hormone receptor alpha −10.22 1.26 1.26 6.49THRA 3,5-diiodothyropropionic acid, amiodarone, thyroxine, L-triiodothyronine Ssc.26215.1.S1_at DNA polymerase epsilon p12 −1.23−2.71 1.19 −1.04 POLE4 gemcitabine subunit (DNA polymerase epsilonsubunit 4) Ssc.23234.1.S1_at collagen, type XXIV, alpha 1 −1.43 1.661.16 1.76 COL24A1 collagenase Ssc.10142.1.A1_at Dihydropyrimidine 2.062.17 1.13 −2.68 DPYD eniluracil dehydrogenase [NADP+] Ssc.3607.1.S1_atInterferon-alpha/beta receptor 2.28 4.65 1.11 −1.56 IFNAR2 interferonbeta-1a, interferon beta alfa-2b, interferon alfacon-1, PEG-interferonalfa-2a, interferon alfa-2a/ribavirin, pegintron, interferon beta-1b,IFNA2A Ssc.14475.3.S1_a_at Peroxisome proliferator 13.83 −9.38 1.09−2.85 PPARG rosiglitazone, GI262570, activated receptor gammapioglitazone, tesaglitazar, (PPAR-gamma) troglitazone Ssc.5000.1.A1_atReceptor protein-tyrosine −1.04 −4.15 1.08 2.25 ERBB2 trastuzumab,BMS-599626, ARRY- kinase erbB-2 334543, XL647, CP-724,714, HKI- 272,lapatinib, erlotinib Ssc.23505.1.S1_at Amine oxidase [flavin- −1.86 2.171.08 1.20 MAOA ladostigil, 1-ethylphenoxathiin containing] A (Monoamine10,10-dioxide, dextroamphetamine, oxidase) (MAO-A) procainamide,tranylcypromine, phenelzine, isocarboxazid, benzphetamine, N-(2-indanyl)glycinamide Ssc.19379.1.A1_at Voltage-dependent L-type 1.83−1.34 1.07 −3.27 CACNA1C clevidipine, MEM-1003, calcium channel alpha-1Camlodipine/olmesartan medoxomil, amlodipine/benazepril, diltiazem,verapamil, mibefradil, bepridil, enalapril/felodipine,amlodipine/atorvastatin, nisoldipine, isradipine, felodipine,nimodipine, nitrendipine, amlodipine, nicardipine, nifedipine,trandolapril/verapamil, diltiazem/enalapril Ssc.6713.1.S1_at Androgenreceptor −1.47 −11.56 1.07 −2.36 AR estradiol valerate/testosterone(Dihydrotestosterone receptor) enanthate, estradiolcypionate/testosterone cypionate, bicalutamide, flutamide, nandrolonedecanoate, testosterone cypionate, medroxyprogesterone acetate,oxandrolone, danazol, stanozolol, spironolactone, testosterone,oxymetholone, testosterone propionate, testosterone enanthateSsc.28329.1.S1_at DNA polymerase beta 1.14 1.19 1.07 5.25 POLBnelarabine, clofarabine, stavudine, trifluridine, vidarabine,zalcitabine, entecavir Ssc.25040.1.S1_at Serine/threonine-protein −3.751.11 1.06 −2.45 CHEK1 UCN-01 (7-hydroxystaurosporine) kinase Chk1Ssc.9781.1.S1_at Plasminogen activator −1.55 −1.17 1.04 1.30 SERPINE1drotrecogin alfa inhibitor-1 (PAI-1) (Endothelial plasminogen activatorinhibitor) (PAI) Ssc.16532.1.S1_at Cell division protein kinase 2 −1.83−1.51 1.04 1.35 CDK2 BMS-387032, flavopiridol (p33 protein kinase).Ssc.22797.1.S1_at DNA topoisomerase II, beta 3.15 −1.87 1.02 −2.91 TOP2Bnovobiocin, etoposide, CPI- 0004Na, pixantrone, becatecarin,elsamitrucin, AQ4N, BN 80927, tafluposide, mitoxantrone, norfloxacin,dexrazoxane, tirapazamine, TAS-103, XK469, gatifloxacin, valrubicin,gemifloxacin, moxifloxacin, nemorubicin, nalidixic acid, epirubicin,doxorubicin, daunorubicin Ssc.14488.1.S1_at Glutamate carboxypeptidaseII −1.04 1.10 1.02 1.69 FOLH1 capromab pendetide

TABLE 6 Day 180 prescription. Fold Fold Fold Fold Change Change ChangeChange D7/ D21/ D60/ D180/ Gene Probe ID Name Base Base Base Base SymbolDRUGS Ssc.11051.1.S1_at Cell division protein kinase 4 1.44 −7.67 −4.9623.75 CDK4 PD-0332991, flavopiridol Ssc.28690.1.A1_at Histonedeacetylase 6 (HD6) −1.92 −1.57 −3.58 20.60 HDAC6 tributyrin, PXD101,pyroxamide, vorinostat, FR 901228 Ssc.21108.1.S1_at Complement C5 −17.353.21 618.80 9.28 C5 eculizumab Ssc.5569.1.S1_at Thyroid hormone receptoralpha −10.22 1.26 1.26 6.49 THRA 3,5-diiodothyropropionic acid,amiodarone, thyroxine, L- triiodothyronine Ssc.1498.1.S1_at Proteasomesubunit beta type 5 −1.81 1.19 1.38 5.94 PSMB5 bortezomibSsc.13460.1.A1_at Histone deacetylase 9 (HD9) −6.40 5.13 −1.79 5.72HDAC9 tributyrin, PXD101, pyroxamide, (HD7B) (HD7). vorinostat, FR901228 Ssc.28329.1.S1_at DNA polymerase beta 1.14 1.19 1.07 5.25 POLBnelarabine, clofarabine, stavudine, trifluridine, vidarabine,zalcitabine, entecavir Ssc.23793.1.S1_at T-cell surface antigen CD2−3.27 79.25 93.34 5.20 CD2 alefacept, siplizumab Ssc.12845.1.S1_at Celldivision protein kinase 6 −6.56 5.40 4.77 5.13 CDK6 PD-0332991,flavopiridol Ssc.24528.1.S1_at Angiotensin-converting enzyme −1.61 5.012.33 4.76 ACE pentopril, perindoprilat, amlodipine/benazepril,lisinopril/hydrochlorothiazide, benazepril, enalapril, perindopril,captopril, enalapril/felodipine, hydrochlorothiazide/moexipril,benazepril/hydrochlorothiazide, hydrochlorothiazide/quinapril,fosinopril/hydrochlorothiazide, captopril/hydrochlorothiazide,enalapril/hydrochlorothiazide, ramipril, moexipril, quinapril,lisinopril, enalaprilat, trandolapril, trandolapril/verapamil,diltiazem/enalapril, fosinopril Ssc.3040.1.S1_at Histone deacetylase 2(HD2) −3.24 2.79 4.94 4.72 HDAC2 tributyrin, PXD101, pyroxamide,vorinostat, FR 901228 Ssc.30373.1.A1_at cGMP-specific 3′,5′-cyclic 4.271.52 2.34 4.09 PDE5A dyphylline, nitroglycerin, DA- phosphodiesterase8159, aminophylline, sildenafil, dipyridamole, aspirin/dipyridamole,vardenafil, tolbutamide, tadalafil, theophylline, pentoxifyllineSsc.2714.1.S1_a_at Proto-oncogene tyrosine- −4.26 9.56 12.54 3.93 FYNdasatinib protein kinase FYN Ssc.12937.1.S1_at Presenilin 1 (PS-1) (S182−14.09 6.21 2.48 3.79 PSEN1 (R)-flurbiprofen protein). Ssc.19937.1.S1_atInosine-5′-monophosphate 1.00 2.69 −1.47 3.65 IMPDH2 thioguanine,VX-944, interferon dehydrogenase 2 alfa-2a/ribavirin, mycophenolic acid,ribavirin Ssc.16114.1.S1_at Dihydropyridine-sensitive L- −1.96 −4.182.24 3.65 CACNA2D1 bepridil, amlodipine, type, calcium channel alpha-pregabalin 2/delta SscAffx.20.1.S1_at T-cell surface glycoprotein −2.1914.07 10.96 3.62 CD3G visilizumab, MT103 CD3 gamma chainSsc.20685.1.S1_at Apoptosis regulator Bcl-2 −2.22 2.77 2.58 3.25 BCL2oblimersen, (−)-gossypol Ssc.11443.1.A1_at Transcription factor p65−1.43 −2.45 −3.96 3.24 RELA NF-kappaB decoy Ssc.26290.1.S1_at Integrinbeta-5 −1.06 −1.51 −5.43 3.24 ITGB5 EMD121974 Ssc.15932.1.S1_at Integrinalpha-V −6.15 5.79 2.94 3.14 ITGAV abciximab, CNTO 95, EMD121974Ssc.14471.1.S1_at B-lymphocyte antigen CD19 9.54 3.30 −10.32 3.04 CD19combotox, HD37-dgRTA, MT103 Ssc.16167.1.S1_at Rho-associated proteinkinase 1 2.40 2.32 2.83 3.00 ROCK1 fasudil, Y-27632 Ssc.26200.1.S1_atThyroid hormone receptor beta- 3.49 −1.56 7.96 2.52 THRB3,5-diiodothyropropionic acid, 1. amiodarone, thyroxine, L-triiodothyronine Ssc.3059.1.S1_at Aldose reductase (Aldehyde −1.74 1.98−1.66 2.49 AKR1B1 sorbinil, Zopolrestat (Alond, reductase). Pfizer),zenarestat (Fujisawa, Parke-Davis) Ssc.11246.1.A1_at Protein kinase C,alpha −5.96 −4.78 2.68 2.46 PRKCA L-threo-safingol Ssc.10256.1.A1_atcAMP-specific 3′,5′-cyclic −1.89 6.74 2.20 2.44 PDE4B dyphylline,nitroglycerin, phosphodiesterase 4B arofylline, tetomilast, L 869298,aminophylline, anagrelide, cilomilast, milrinone, rolipram,dipyridamole, L-826,141, roflumilast, tolbutamide, theophylline,pentoxifylline, caffeine Ssc.1598.1.S1_at Retinoic acid receptor RXR-−2.21 −1.13 −4.20 2.42 RXRB bexarotene, retinoic acid, 9- betacis-retinoic acid Ssc.1520.1.A1_at Proto-oncogene tyrosine- −1.05 −1.882.00 2.39 RET sunitinb protein kinase receptor ret Ssc.11572.1.A1_atHistone deacetylase 3 (HD3) −1.65 1.67 −1.55 2.36 HDAC3 tributyrin,PXD101, pyroxamide, (RPD3-2) (SMAP45). MGCD0103, vorinostat, FR 901228Ssc.18051.1.S1_at cGMP-inhibited 3′,5′-cyclic −3.16 1.96 3.41 2.32 PDE3Bdyphylline, nitroglycerin, phosphodiesterase B medorinone,aminophylline, cilostazol, dipyridamole, amrinone, tolbutamide,theophylline, pentoxifylline Ssc.15886.1.S1_at Apopain precursor(Caspase-3) −3.02 3.64 2.31 2.29 CASP3 IDN-6556 (CASP-3)Ssc.5000.1.A1_at Receptor protein-tyrosine −1.04 −4.15 1.08 2.25 ERBB2trastuzumab, BMS-599626, ARRY- kinase erbB-2 334543, XL647, CP-724,714,HKI- 272, lapatinib, erlotinib Ssc.15374.1.S1_at COL14A1 protein 1.10−17.71 3.79 2.24 COL14A1 collagenase Ssc.19873.1.S1_at Collagen alpha1(XVII) chain −2.37 3.02 −1.55 2.18 COL17A1 collagenaseSsc.19532.1.S1_at Guanylate cyclase soluble, −4.28 12.74 3.04 2.13GUCY1B3 nitroglycerin, isosorbide-5- beta-1 chain mononitrate,isosorbide dinitrate, nitroprusside, isosorbide dinitrate/hydralazineSsc.5045.1.S1_at 3-beta-hydroxysteroid- −1.55 1.24 2.19 2.08 EBP SR31747 delta(8),delta(7)-isomerase (EC 5.3.3.5) (Cholestenoldelta-isomerase) (Emopamil- binding protein). Ssc.9272.1.S1_atTumor-associated calcium 1.81 3.94 176.50 2.07 TACSTD1 tucotuzumabcelmoleukin signal transducer 1 (EPCAM antigen) Ssc.7139.1.S1_atDihydrofolate reductase −1.13 1.41 −1.12 2.06 DHFR pyrimethamine,trimethoprim, iclaprim, methotrexate, sulfisoxazole, triamterene, folicacid, trimetrexate, LY231514, PT 523 Ssc.818.1.S1_at RAF proto-oncogene−1.40 2.56 1.58 1.98 RAF1 sorafenib serine/threonine-protein kinaseSsc.25168.1.S1_a_at Collagen alpha 1(XVI) chain −7.23 −3.61 −4.45 1.87COL16A1 collagenase Ssc.3737.1.S1_at Tubulin gamma-1 chain (Gamma-1−1.24 −1.88 −1.29 1.82 TUBG1 epothilone B, ixabepilone, tubulin) (colchicine/probenecid, XRP9881, E7389, AL 108, EC145, NPI-2358,milataxel, TPI 287, TTI-237, docetaxel, vinflunine, vinorelbine,vincristine, vinblastine, paclitaxel, podophyllotoxin, colchicineSsc.23234.1.S1_at collagen, type XXIV, alpha 1 −1.43 1.66 1.16 1.76COL24A1 collagenase Ssc.16000.1.A1_at Vascular endothelial growth 1.08−3.40 3.34 1.72 FLT1 sunitinib, axitinib, CEP 7055 factor receptor 1Ssc.14488.1.S1_at Glutamate carboxypeptidase II −1.04 1.10 1.02 1.69FOLH1 capromab pendetide Ssc.7176.1.A1_at C—X—C chemokine receptor type3.74 10.91 8.15 1.68 CXCR4 JM 3100 4 (CXC-R4) (CXCR-4) Ssc.10287.1.A1_atTransforming growth factor 1.41 −4.54 1.43 1.67 TGFB2 AP-12009 beta 2Ssc.7111.1.A1_at Ribonucleoside-diphosphate −13.13 4.08 1.37 1.67 RRM2gemcitabine, triapine, reductase M2 chain hydroxyurea, fludarabinephosphate Ssc.9595.1.S1_at Beta platelet-derived growth 3.48 −3.60 1.401.65 PDGFRB dasatinib, sunitinib, axitinib, factor receptor KRN-951,imatinib, sorafenib, becaplermin Ssc.5826.1.A1_at Macrophage colonystimulating 1.93 −4.97 −13.18 1.61 CSF1R sunitinib factor I receptorSsc.17518.1.S1_at Adenosine A1 receptor −3.16 3.44 −1.56 1.58 ADORA1adenosine, dyphylline, aminophylline, clofarabine, theophylline,caffeine, tecadenoson Ssc.19691.1.S1_at Platelet-activating factor 1.591.16 3.01 1.47 PLA2G7 darapladib acetylhydrolase Ssc.9523.1.A1_atMethylated-DNA--protein- 1.55 −1.17 3.35 1.47 MGMT O6-benzylguaninecysteine methyltransferase Ssc.11406.1.A1_a_at Interleukin-1 receptor,type I 1.03 2.70 −2.44 1.42 IL1R1 anakinra Ssc.11085.1.S1_atGlucagon-like peptide 2 −1.08 −1.17 −1.26 1.40 GLP2R teduglutidereceptor Ssc.10591.1.A1_at Metabotropic glutamate −7.83 1.54 −1.31 1.40GRM5 fasoracetam receptor 5 Ssc.9034.1.A1_at Proteinase activatedreceptor 1 −1.29 3.75 −1.40 1.37 F2R chrysalin, argatroban, bivalirudinSsc.10360.1.S1_at B-Raf proto-oncogene −2.15 1.26 3.09 1.36 BRAFsorafenib serine/threonine-protein kinase Ssc.16532.1.S1_at Celldivision protein kinase 2 −1.83 −1.51 1.04 1.35 CDK2 BMS-387032,flavopiridol Ssc.9781.1.S1_at Plasminogen activator −1.55 −1.17 1.041.30 SERPINE1 drotrecogin alfa inhibitor-1 precursor (PAI-1)(Endothelial plasminogen activator inhibitor) (PAI) Ssc.26328.1.S1_atC-C chemokine receptor type 5 −2.53 5.61 3.25 1.29 CCR5 maraviroc,vicriviroc, SCH (CCR5) (CD195 antigen) 351125 Ssc.8046.1.A1_atpeptidylprolyl isomerase A 1.16 −1.08 1.39 1.26 PPIAN-methyl-4-Ile-cyclosporin isoform 1; cyclophilin A; Ssc.11302.1.S1_atCollagen alpha 1(III) chain −1.80 2.02 2.06 1.26 COL3A1 collagenaseSsc.13186.1.S1_at Cell division protein kinase 7 −1.08 2.38 4.34 1.24CDK7 BMS-387032, flavopiridol Ssc.27603.1.S1_at Endothelin B receptor5.30 −3.27 15.99 1.23 EDNRB bosentan, sitaxsentan, atrasentanSsc.27093.1.A1_at cAMP-specific 3′,5′-cyclic −6.34 −2.27 −7.97 1.23PDE4C dyphylline, nitroglycerin, phosphodiesterase 4C arofylline,tetomilast, L869298, aminophylline, anagrelide, cilomilast, milrinone,rolipram, dipyridamole, L-826,141, roflumilast, tolbutamide,theophylline, pentoxifylline, caffeine Ssc.20904.1.A1_at RAC-gammaserine/threonine- −1.34 3.01 −2.18 1.23 AKT3 enzastaurin protein kinaseSsc.23505.1.S1_at Amine oxidase [flavin- −1.86 2.17 1.08 1.20 MAOAladostigil, 1-ethylphenoxathiin containing] A (Monoamine 10,10-dioxide,oxidase) (MAO-A) dextroamphetamine, procainamide, tranylcypromine,phenelzine, isocarboxazid, benzphetamine, N- (2-indanyl)glycinamideSsc.15312.1.S1_at Histone deacetylase 4 (HD4) −1.93 2.85 −2.41 1.20HDAC4 tributyrin, PXD101, pyroxamide, vorinostat, FR 901228Ssc.9019.1.A1_at Atrial natriuretic peptide −1.09 −1.69 5.31 1.18 NPR3nesiritide clearance receptor Ssc.16160.1.S1_at T lymphocyte activation−1.55 3.88 −1.37 1.18 CD86 abatacept antigen CD86 Ssc.1844.1.S1_atAtrial natriuretic peptide −1.94 −1.06 −1.63 1.13 NPR2 nesiritidereceptor B Ssc-11171.1.S1_at Adenosine deaminase 1.32 −2.04 −3.23 1.12ADA pentostatin, vidarabine Ssc.16823.1.S1_at P2Y purinoceptor 12(P2Y12) 1.38 1.19 1.41 1.11 P2RY12 prasugrel, AZD 6140, (P2Y12 plateletADP receptor) clopidogrel Ssc.19700.1.S1_at Serine/threonine protein1.11 1.13 1.34 1.09 PPP3CB ISAtx-247, tacrolimus, phosphatase 2Bcatalytic pimecrolimus, cyclosporin A subunit, beta Ssc.26752.1.S1_at5-hydroxytryptamine −3.57 1.22 1.60 1.08 HTR3B cisapride, granisetron,(serotonin) receptor 3B ondansetron, fenfluramine, palonosetron,mirtazapine, alosetron, D-tubocurarine, ergotamine, dolasetronSsc.6418.1.S1_at Farnesyl-diphosphate −1.25 2.31 1.33 1.08 FDFT1TAK-475, zoledronic acid farnesyltransferase Ssc.22477.1.S1_at Collagenalpha 1(IV) chain 1.58 −5.08 −1.78 1.04 COL4A1 collagenaseSsc.31192.1.S1_at Collagen alpha 1(XVIII) chain −1.89 −1.36 −19.06 1.03COL18A1 collagenase Ssc.1091.1.S1_at Collagen alpha 1(I) chain −3.27−17.59 2.07 1.03 COL1A1 collagenase Ssc.7581.1.A1_at FL cytokinereceptor 1.69 1.04 −1.81 1.01 FLT3 CHIR-258, sorafenib, lestaurtinib,CGP 41251

TABLE 7 Upregulated gene targets at all timepoints (Days 7, 21, 60, and180 relative to baseline) of PAH progression with available drugs FoldFold Fold Fold Change Change Change Change D7/ D21/ D60/ D180/ GeneProbe ID Name Base Base Base Base Symbol Drugs Ssc.28329.1.S1_at DNApolymerase beta 1.14 1.19 1.07 5.25 POLB nelarabine, clofarabine,stavudine, trifluridine, vidarabine, zalcitabine, entecavirSsc.9272.1.S1_at Tumor-associated 1.81 3.94 176.50 2.07 TACSTD1tucotusumab celmoleukin calcium signal transducer 1 (EPCAM antigen)Ssc.7176.1.A1_at C—X—C chemokine 3.74 10.91 8.15 1.68 CXCR4 JM 3100(1,1′-(1,4- receptor type 4 phenylenebis{methylene)}bis(1,4, (CXC-R4)(CXCR-4) 8,11- (CD184 antigen)tetraazacyclotetradecane)octahydrochloride dihydrate) Ssc.19691.1.S1_atPlatelet-activating 1.59 1.16 3.01 1.47 PLA2G7 darapladib factoracetylhydrolase Ssc.16823.1.S1_at P2Y purinoceptor 12 1.38 1.19 1.411.11 P2RY12 prasugrel, AZD 6140 (P2Y12) (Ticagrelor), clopidogrelSsc.19700.1.S1_at Serine/threonine 1.11 1.13 1.34 1.09 PPP3CBISAtx-247,tacrolimus, protein phosphatase pimecrolimus, cyclosporin A 2Bcatalytic subunit, beta isoform Ssc.14258.1.S1_at Amyloid beta A4 1.873.33 1.34 −1.02 APP Bapineuzumab (AAB-001) protein Ssc.8726.1.A1_atAmidophosphoribosyltransferase 1.03 1.24 4.16 −1.11 PPAT thioguanine,azathioprine, 6- mercaptopurine,

TABLE 8 Upregulated gene targets at Days 21 and 60 (relative tobaseline) of PAH progression with available drugs Fold Fold Fold FoldChange Change Change Change D180/ Probe ID Name D7/Base D21/BaseD60/Base Base Ssc.21108.1.S1_at Complement C5 −17.35 3.21 618.80 9.28Ssc.9272.1.S1_at Tumor-associated 1.81 3.94 176.50 2.07 calcium signaltransducer 1 Ssc.23793.1.S1_at T-cell surface −3.27 79.25 93.34 5.20antigen CD2 Ssc.17245.1.S1_at Interleukin-13 −1.99 23.04 21.92 7.16receptor alpha-1 chain Ssc.15999.1.A1_at Vascular endothelial 1.24 1.2418.52 −11.02 growth factor receptor 2 Ssc.2714.1.S1_a_at Proto-oncogene−4.26 9.56 12.54 3.93 tyrosine-protein kinase FYN SscAffx.20.1.S1_atT-cell surface −2.19 14.07 10.96 3.62 glycoprotein CD3 gamma chainSsc.7176.1.A1_at C—X—C chemokine 3.74 10.91 8.15 1.68 receptor type 4(CXC-R4) (CXCR-4) ( Ssc.7297.1.S1_at Amine oxidase 1.16 6.42 7.02 −1.13[flavin-containing] B (EC 1.4.3.4) (Monoamine oxidase) (MAO-B).Ssc.20438.1.S1_at Prostaglandin F2- −3.20 2.13 5.28 −38.97 alphareceptor (PGF2 alpha receptor). Ssc.3040.1.S1_at Histone deacetylase−3.24 2.79 4.94 4.72 2 (HD2). Ssc.12845.1.S1_at Cell division −6.56 5.404.77 5.13 protein kinase 6 (E Ssc.13186.1.S1_at Cell division −1.08 2.384.34 1.24 protein kinase 7 Ssc.8726.1.A1_atAmidophosphoribosyltransferase 1.03 1.24 4.16 −1.11 Ssc.15878.1.S1_atSerine/threonine 1.85 3.22 3.62 −1.49 protein phosphatase 2B catalyticsubunit, alpha isoform Ssc.26351.1.S1_at cAMP-specific 3′,5′- 4.67 4.993.61 −1.15 cyclic phosphodiesterase 4D (EC 3.1.4.17) (DPDE3) (PDE43).[Source: Uniprot/SWISSPROT; Acc: Q08499] Ssc.15801.1.A1_at Proteinkinase C, 3.36 6.36 3.53 −4.98 beta type (EC 2.7.1.37) (PKC-beta)(PKC-B). [Source: Uniprot/SWISSPROT; Acc: P05771] Ssc.24966.1.S1_atPurine nucleoside −3.34 3.12 3.46 −1.14 phosphorylase Ssc.18051.1.S1_atcGMP-inhibited −3.16 1.96 3.41 2.32 3′,5′-cyclic phosphodiesterase BSsc.26328.1.S1_at C-C chemokine −2.53 5.61 3.25 1.29 receptor type 5(C-C CKR-5) (CC-CKR-5) (CCR-5) (CCR5) (HIV- 1 fusion coreceptor)(CHEMR13) (CD195 antigen). [Source: Uniprot/SWISSPROT; Acc: P51681]Ssc.17224.1.S1_at Toll-like receptor 8 1.17 6.49 3.13 −1.52 precursor.[Source: Uniprot/SWISSPROT; Acc: Q9NR97] Ssc.21011.1.S1_at Collagenalpha 2(I) −2.70 1.24 3.12 −1.01 chain precursor. [Source:Uniprot/SWISSPROT; Acc: P08123] Ssc.10360.1.S1_at B-Raf proto-oncogene−2.15 1.26 3.09 1.36 serine/threonine- protein kinase (v- Raf murinesarcoma viral oncogene homolog B1). Ssc.19532.1.S1_at Guanylate cyclase−4.28 12.74 3.04 2.13 soluble, beta-1 Ssc.19691.1.S1_atPlatelet-activating 1.59 1.16 3.01 1.47 factor acetylhydrolaseSsc.17155.1.A1_at heparanase; 4.81 5.38 2.98 −1.83 heparanase-1Ssc.15932.1.S1_at Integrin alpha-V −6.15 5.79 2.94 3.14Ssc.11381.1.S1_at Interferon- 10.45 8.08 2.61 −1.30 alpha/beta receptoralpha chain precursor (IFN- alpha-REC). [Source: Uniprot/SWISSPROT; Acc:P17181] Ssc.20685.1.S1_at Apoptosis regulator −2.22 2.77 2.58 3.25Bcl-2. [Source: Uniprot/SWISSPROT; Acc: P10415] Ssc.12937.1.S1_atPresenilin 1 (PS-1) −14.09 6.21 2.48 3.79 (S182 protein).Ssc.6801.1.S1_at Proto-oncogene −1.06 1.69 2.36 −1.82 tyrosine-proteinkinase YES Ssc.24528.1.S1_at Angiotensin- −1.61 5.01 2.33 4.76converting enzyme Ssc.15886.1.S1_at Apopain (Caspase-3) −3.02 3.64 2.312.29 (CASP-3 Ssc.10256.1.A1_at cAMP-specific 3′,5′- −1.89 6.74 2.20 2.44cyclic phosphodiesterase 4B Ssc.5045.1.S1_at 3-beta- −1.55 1.24 2.192.08 hydroxysteroid- delta(8),delta(7)- isomerase Ssc.16145.1.A1_at5-hydroxytryptamine 1.08 2.10 2.15 5.45 2B receptor (5-HT- 2B)(Serotonin receptor 2B). Ssc.16186.1.S1_at T-cell surface 9.00 3.12 2.12−5.66 glycoprotein CD3 epsilon chain Ssc.11302.1.S1_at Collagen alpha−1.80 2.02 2.06 1.26 1(III) chain precursor. Ssc.19673.1.S1_at T-cellsurface 6.40 2.70 2.03 −11.77 glycoprotein CD3 delta chain precursor(T-cell receptor T3 delta chain). Ssc.6710.1.A1_at Ribonucleoside- −1.901.44 2.01 −1.01 diphosphate reductase M1 chain (Ribonucleotide reductaselarge chain Ssc.11147.1.S1_at Aldehyde 3.18 1.13 2.00 −1.68dehydrogenase, mitochondrial precursor (ALDH class 2) (ALDHI) (ALDH-E2).Ssc.15739.1.S1_at Cytokine receptor −1.12 9.42 1.90 −1.28 common gammachain (Interleukin-2 receptor gamma chain) (IL-2R gamma chain) (CD132antigen). Ssc.15822.1.S1_at Coagulation factor V 1.92 3.76 1.89 −1.75precursor (Activated protein C cofactor). Ssc.4756.1.A1_at Adenosine A32.15 2.10 1.88 −1.81 receptor. Ssc.12791.1.A1_at 3-hydroxy-3- 3.27 2.771.77 −2.56 methylglutaryl- coenzyme A reductase Ssc.818.1.S1_at RAFproto-oncogene −1.40 2.56 1.58 1.98 serine/threonine- protein kinaseSsc.16823.1.S1_at P2Y purinoceptor 12 1.38 1.19 1.41 1.11 (P2Y12) (P2Y12platelet ADP receptor) Ssc.9565.1.S1_at Interferon-gamma 2.92 1.63 1.41−1.23 receptor alpha chain (CD119 antigen) Ssc.1498.1.S1_at Proteasomesubunit −1.81 1.19 1.38 5.94 beta type 5 Ssc.7111.1.A1_atRibonucleoside- −13.13 4.08 1.37 1.67 diphosphate reductase M2 chainSsc.19700.1.S1_at Serine/threonine 1.11 1.13 1.34 1.09 proteinphosphatase 2B catalytic subunit, beta Ssc.14258.1.S1_at Amyloid beta A41.87 3.33 1.34 −1.02 protein Ssc.6418.1.S1_at Farnesyl-diphosphate −1.252.31 1.33 1.08 farnesyltransferase Ssc.5569.1.S1_at Thyroid hormone−10.22 1.26 1.26 6.49 receptor alpha (C- erbA-alpha) (c-erbA- 1)Ssc.23234.1.S1_at collagen, type XXIV, −1.43 1.66 1.16 1.76 alpha 1Ssc.10142.1.A1_at Dihydropyrimidine 2.06 2.17 1.13 −2.68 dehydrogenase[NADP+] Ssc.3607.1.S1_at Interferon- 2.28 4.65 1.11 −1.56 alpha/betareceptor beta chain Ssc.23505.1.S1_at Amine oxidase −1.86 2.17 1.08 1.20[flavin-containing] A Ssc.28329.1.S1_at DNA polymerase 1.14 1.19 1.075.25 Ssc.25040.1.S1_at Serine/threonine- −3.75 1.11 1.06 −2.45 proteinkinase Chk1 Ssc.26379.1.S1_at Glutamate [NMDA] −1.32 1.37 1.03 −2.59receptor subunit epsilon 3 Ssc.14488.1.S1_at Glutamate −1.04 1.10 1.021.69 carboxypeptidase II Gene Probe ID Symbol Drugs Ssc.21108.1.S1_at C5eculizumab Ssc.9272.1.S1_at TACSTD1 tucctuzumab celmoleukinSsc.23793.1.S1_at CD2 alefacept, siplizumab Ssc.17245.1.S1_at IL13RA1cintredekin besudotox Ssc.15999.1.A1_at KDR AEE 788, sunitinib, AZD2171, pazopanib, XL647, CEP 7055, BMS-582664, KRN-951, vatalanib,sorafenib, vandetanib, pegaptanib Ssc.2714.1.S1_a_at FYN dasatinibSscAffx.20.1.S1_at CD3G visilizumab, MT103 Ssc.7176.1.A1_at CXCR4 JM3100 Ssc.7297.1.S1_at MAOB safinamide, ladostigil, rasagiline,selegiline, dextroamphetamine, procainamide, tranylcypromine,phenelzine, isocarboxazid, benzphetamine Ssc.20438.1.S1_at PTGFRtafluprost, travoprost, isopropyl unoprostone, bimatoprost, latanoprostSsc.3040.1.S1_at HDAC2 tributyrin, PXD101, pyroxamide, vorinostat, FR901228 Ssc.12845.1.S1_at CDK6 PD-0332991, flavopiridol Ssc.13186.1.S1_atCDK7 BMS-387032, flavopiridol Ssc.8726.1.A1_at PPAT 6-mercaptopurine,thioguanine, azathioprine Ssc.15878.1.S1_at PPP3CA ISAtx-247,tacrolimus, pimecrolimus, cyclosporin A Ssc.26351.1.S1_at PDE4Ddyphylline, nitroglycerin, arofylline, tetomilast, L 869298,aminophylline, anagrelide, cilomilast, milrinone, rolipram,dipyridamole, L-826,141, roflumilast, tolbutamide, theophylline,pentoxifylline, caffeine Ssc.15801.1.A1_at PRKCB1 enzastaurin,ruboxistaurin Ssc.24966.1.S1_at NP forodesine, 9-deaza-9-(3-thienylmethyl)guanine Ssc.18051.1.S1_at PDE3B dyphylline, nitroglycerin,medorinone, aminophylline, cilostazol, dipyridamole, amrinone,tolbutamide, theophylline, pentoxifylline Ssc.26328.1.S1_at CCR5maraviroc, vicriviroc, SCH 351125 Ssc.17224.1.S1_at TLR8 resiquimodSsc.21011.1.S1_at COL1A2 collagenase Ssc.10360.1.S1_at BRAF sorafenibSsc.19532.1.S1_at GUCY1B3 nitroglycerin, isosorbide-5-mononitrate,isosorbide dinitrate, nitroprusside, isosorbide dinitrate/hydralazineSsc.19691.1.S1_at PLA2G7 darapladib Ssc.17155.1.A1_at HPSE heparanaseinhibitor PI-88 Ssc.15932.1.S1_at ITGAV abciximab, CNTO 95, EMD121974(Cilengitide) Ssc.11381.1.S1_at IFNAR1 interferon beta-1a, interferonalfa-2b, interferon alfacon-1, PEG-interferon alfa- 2a, interferonalfa-2a/ribavirin, pegintron, interferon beta-1b, IFNA2ASsc.20685.1.S1_at BCL2 Oblimersen (Augmerosen), Ssc.12937.1.S1_at PSEN1(R)-flurbiprofen (Tarenflurbil) Ssc.6801.1.S1_at YES1 dasatinibSsc.24528.1.S1_at ACE pentopril, perindoprilat, amlodipine/benazepril,lisinopril/hydrochlorothiazide, benazepril, enalapril, perindopril,captopril, enalapril/felodipine, hydrochlorothiazide/moexipril,benazepril/hydrochlorothiazide, hydrochlorothiazide/quinapril,fosinopril/hydrochlorothiazide, captopril/hydrochlorothiazide,enalapril/hydrochlorothiazide, ramipril, moexipril, quinapril,lisinopril, enalaprilat, trandolapril, trandolapril/verapamil,diltiazem/enalapril, fosinopril Ssc.15886.1.S1_at CASP3 IDN-6556Ssc.10256.1.A1_at PDE4B dyphylline, nitroglycerin, arofylline,tetomilast, L 869298, aminophylline, anagrelide, cilomilast, milrinone,rolipram, dipyridamole, L-826,141, roflumilast, tolbutamide,theophylline, pentoxifylline, caffeine Ssc.5045.1.S1_at EBP SR 31747Ssc.16145.1.A1_at HTR2B risperidone, buspirone, blonanserin, asenapine,eletriptan, epinastine, fenfluramine, quetiapine, nefazodone,mirtazapine, dihydroergotamine, apomorphine, ergotamineSsc.16186.1.S1_at CD3E visilizumab, MT103, muromonab-CD3Ssc.11302.1.S1_at COL3A1 collagenase Ssc.19673.1.S1_at CD3D visilizumab,MT103 Ssc.6710.1.A1_at RRM1 gemcitabine, clofarabine, fludarabinephosphate Ssc.11147.1.S1_at ALDH2 disulfiram, chlorpropamideSsc.15739.1.S1_at IL2RG aldesleukin, denileukin diftitoxSsc.15822.1.S1_at F5 drotrecogin alfa Ssc.4756.1.A1_at ADORA3 adenosine,dyphylline, aminophylline, clofarabine, theophylline, caffeineSsc.12791.1.A1_at HMGCR aspirin/pravastatin, lovastatin/niacin,ezetimibe/simvastatin, amlodipine/atorvastatin, fluvastatin,cerivastatin, atorvastatin, pravastatin, simvastatin, lovastatin,rosuvastatin Ssc.818.1.S1_at RAF1 sorafenib Ssc.16823.1.S1_at P2RY12prasugrel, AZD 6140 (Ticagrelor), clopidogrel Ssc.9565.1.S1_at IFNGR1interferon gamma-1b Ssc.1498.1.S1_at PSMB5 bortezomib Ssc.7111.1.A1_atRRM2 gemcitabine, triapine, hydroxyurea, fludarabine phosphateSsc.19700.1.S1_at PPP3CB ISAtx-247, tacrolimus, pimecrolimus,cyclosporin A Ssc.14258.1.S1_at APP AAB-001 (Bapineuzumab)Ssc.6418.1.S1_at FDFT1 TAK-475, zoledronic acid Ssc.5569.1.S1_at THRA3,5-diiodothyropropionic acid, amiodarone, thyroxine, L-triiodothyronineSsc.23234.1.S1_at COL24A1 collagenase Ssc.10142.1.A1_at DPYD eniluracilSsc.3607.1.S1_at IFNAR2 interferon beta-1a, interferon alfa-2b,interferon alfacon-1, PEG-interferon alfa- 2a, interferonalfa-2a/ribavirin, pegintron, interferon beta-1b, IFNA2ASsc.23505.1.S1_at MAOA ladostigil, 1-ethylphenoxathiin 10,10- dioxide,dextroamphetamine, procainamide, tranylcypromine, phenelzine,isocarboxazid, benzphetamine, N-(2- indanyl)glycinamideSsc.28329.1.S1_at POLB nelarabine, clofarabine, stavudine, trifluridine,vidarabine, zalcitabine, entecavir Ssc.25040.1.S1_at CHEK1 UCN-01(7-hydroxystaurosporine) Ssc.26379.1.S1_at GRIN2Cdextromethorphan/guaifenesin, morphine/dextromethorphan, neramexane, SPM927, bicifadine, delucemine, CR 2249, besonprodil, UK-240455, ketamine,felbamate, memantine, orphenadrine, cycloserine,N-(2-indanyl)glycinamide, dextromethorphan,brompheniramine/dextromethorphan/pseudoephedrine,chlorpheniramine/dextromethorphan/phenylephrine,carbinoxamine/dextromethorphan/pseudoephedrine,dextromethorphan/promethazine, 1- aminocyclopropane-1-carboxylic acidSsc.14488.1.S1_at FOLH1 capromab pendetide

TABLE 9 Upregulated gene targets at Days 21, 60 and 180 (relative tobaseline) of PAH progression with available drugs Fold Fold Fold ChangeChange Change Fold D7/ D21/ D60/ Change Gene Probe ID Name Base BaseBase D180/Base Symbol Drugs Ssc.23793.1.S1_at T-cell surface −3.27 79.2593.34 5.20 CD2 alefacept, siplizumab antigen CD2 SscAffx.20.1.S1_atT-cell surface −2.19 14.07 10.96 3.62 CD3G visilizumab, MT103glycoprotein CD3 gamma chain Ssc.19532.1.S1_at Guanylate cyclase −4.2812.74 3.04 2.13 GUCY1B3 nitroglycerin, isosorbide-5-mononitrate,soluble, beta-1 isosorbide dinitrate, nitroprusside, chain isosorbidedinitrate/hydralazine Ssc.7176.1.A1_at C—X—C chemokine 3.74 10.91 8.151.68 CXCR4 JM 3100 (1,1′-(1,4- receptor type 4phenylenebis(methylene))bis(1,4,8,11- (CXC-R4) (CXCR-4)tetraazacyclotetradecane)octahydrochloride dihydrate) Ssc.2714.1.S1_a_atProto-oncogene −4.26 9.56 12.54 3.93 FYN dasatinib tyrosine-proteinkinase FYN Ssc.10256.1.A1_at cAMP-specific −1.89 6.74 2.20 2.44 PDE4Bdyphylline, nitroglycerin, arofylline, 3′,5′-cyclic tetomilast, L869298, aminophylline, phosphodiesterase anagrelide, cilomilast,milrinone, 4B rolipram, dipyridamole, L-826,141, roflumilast,tolbutamide, theophylline, pentoxifylline, caffeine Ssc.12937.1.S1_atPresenilin 1 (PS-1) −14.09 6.21 2.48 3.79 PSEN1 (R)-flurbiprofen (S182protein). Ssc.15932.1.S1_at Integrin alpha-V −6.15 5.79 2.94 3.14 ITGAVabciximab, CNTO 95, EMD121974 (Cilengitide) Ssc.26328.1.S1_at C-Cchemokine −2.53 5.61 3.25 1.29 CCR5 maraviroc, vicriviroc, SCH 351125receptor type 5 (CCR5) Ssc.12845.1.S1_at Cell division −6.56 5.40 4.775.13 CDK6 PD-0332991, flavopiridol protein kinase 6 Ssc.24528.1.S1_atAngiotensin- −1.61 5.01 2.33 4.76 ACE pentopril, perindoprilat,converting enzyme amlodipine/benazepril, lisinopril/hydrochlorothiazide,benazepril, enalapril, perindopril, captopril, enalapril/felodipine,hydrochlorothiazide/moexipril, benazepril/hydrochlorothiazide,hydrochlorothiazide/quinapril, fosinopril/hydrochlorothiazide,captopril/hydrochlorothiazide, enalapril/hydrochlorothiazide, ramipril,moexipril, quinapril, lisinopril, enalaprilat, trandolapril,trandolapril/verapamil, diltiazem/enalapril, fosinopril Ssc.7130.1.S1_atPhenylalanine-4- 4.70 4.71 11.30 1.48 PAH (6R)-tetrahydrobiopterinhydroxylase Ssc.7111.1.A1_at Ribonucleoside- −13.13 4.08 1.37 1.67 RRM2gemcitabine, triapine, hydroxyurea, diphosphate fludarabine phosphatereductase M2 chain (Ribonucleotide reductase small chain).Ssc.9272.1.S1_at Tumor-associated 1.81 3.94 176.50 2.07 TACSTD1tucotuzumab celmoleukin calcium signal transducer 1 (EPCAM antigen)Ssc.15886.1.S1_at Apopain (Caspase- −3.02 3.64 2.31 2.29 CASP3 IDN-65563) (CASP-3) Ssc.21108.1.S1_at Complement C5 −17.35 3.21 618.80 9.28 C5eculizumab Ssc.3040.1.S1_at Histone deacetylase −3.24 2.79 4.94 4.72HDAC2 tributyrin, PXD101, pyroxamide, 2 (HD2). vorinostat, FR 901228Ssc.20685.1.S1_at Apoptosis regulator −2.22 2.77 2.58 3.25 BCL2oblimersen, (−)-gossypol Bcl-2 Ssc.818.1.S1_at RAF proto-oncogene −1.402.56 1.58 1.98 RAF1 sorafenib serine/threonine- protein kinaseSsc.13186.1.S1_at Cell division −1.08 2.38 4.34 1.24 CDK7 BMS-387032,flavopiridol protein kinase 7 Ssc.6418.1.S1_at Farnesyl- −1.25 2.31 1.331.08 FDFT1 TAK-475, zoledronic acid diphaosphate farnesyltransferaseSsc.23505.1.S1_at Amine oxidase −1.86 2.17 1.08 1.20 MAOA ladostigil,1-ethylphenoxathiin 10,10- (flavin-containing) dioxide,dextroamphetamine, procainamide, A (Monoamine tranylcypromine,phenelzine, oxidase) (MAO-A). isocarboxazid, benzphetamine, N-(2-indanyl)glycinamide Ssc.11302.1.S1_at Collagen alpha −1.80 2.02 2.061.26 COL3A1 collagenase 1(III) chain precursor. Ssc.18051.1.S1_atcGMP-inhibited −3.16 1.96 3.41 2.32 PDE3B dyphylline, nitroglycerin,medorinone, 3′,5′-cyclic aminophylline, cilostazol, dipyridamole,phosphodiesterase B amrinone, tolbutamide, theophylline, pentoxifyllineSsc.23234.1.S1_at collagen, type −1.43 1.66 1.16 1.76 COL24A1collagenase XXIV, alpha 1 Ssc.5569.1.S1_at Thyroid hormone −10.22 1.261.26 6.49 THRA 3,5-diiodothyropropionic acid, receptor alpha amiodarone,thyroxine, L-triiodothyronine Ssc.10360.1.S1_at B-Raf proto- −2.15 1.263.09 1.36 BRAF sorafenib oncogene serine/threonine- protein kinaseSsc.5045.1.S1_at 3-beta- −1.55 1.24 2.19 2.08 EBP SR 31747hydroxysteroid- delta(8),delta(7)- isomerase Ssc.1498.1.S1_at Proteasomesubunit −1.81 1.19 1.38 5.94 PSMB5 bortezomib beta type 5Ssc.28329.1.S1_at DNA polymerase beta 1.14 1.19 1.07 5.25 POLBnelarabine, clofarabine, stavudine, trifluridine, vidarabine,zalcitabine, entecavir Ssc.16823.1.S1_at P2Y purinoceptor 12 1.38 1.191.41 1.11 P2RY12 prasugrel, AZD 6140, clopidogrel (P2Y12) (P2Y12platelet ADP receptor) (P2Y(ADP)) Ssc.19691.1.S1_at Platelet-activating1.59 1.16 3.01 1.47 PLA2G7 darapladib factor acetylhydrolaseSsc.19700.1.S1_at Serine/threonine 1.11 1.13 1.34 1.09 PPP3CB ISAtx-247,tacrolimus, pimecrolimus, protein phosphatase cyclosporin A 2B catalyticsubunit, beta Ssc.14488.1.S1_at Glutamate −1.04 1.10 1.02 1.69 FOLH1capromab pendetide carboxypeptidase II

TABLE 10 Upregulated gene targets at both Days 7 and 21 (relative tobaseline) of PAH progression with available drugs Fold Fold Fold FoldChange Change Change Change Gene Probe ID Name D7/Base D21/Base D60/BaseD180/Base Symbol Drugs Ssc.11381.1.S1_at Interferon-alpha/beta receptor10.45 8.08 2.61 −1.30 IFNAR1 interferon beta-1a, alpha chain interferonalfa-2b, interferon alfacon-1, PEG- interferon alfa-2a, interferonalfa-2a/ribavirin, pegintron, interferon beta- 1b, IFNA2ASsc.16186.1.S1_at T-cell surface glycoprotein 9.00 3.12 2.12 −5.66 CD3Evisilizumab, MT103, CD3 epsilon chain muromonab-CD3 Ssc.19673.1.S1_atT-cell surface glycoprotein 6.40 2.70 2.03 −11.77 CD3D visilizumab,MT103 CD3 delta chain Ssc.17155.1.A1_at heparanase; heparanase-1 4.815.38 2.98 −1.83 HPSE heparanase inhibitor PI-88 Ssc.7130.1.S1_atPhenylalanine-4-hydroxylase 4.70 4.71 11.30 1.48 PAH(6R)-tetrahydrobiopterin Ssc.26351.1.S1_at cAMP-specific 3′,5′-cyclic4.67 4.99 3.61 −1.15 PDE4D dyphylline, nitroglycerin, phosphodiesterase4D arofylline, tetomilast, L869298, aminophylline, anagrelide,cilomilast, milrinone, rolipram, dipyridamole, L-826,141, roflumilast,tolbutamide, theophylline, pentoxifylline, caffeine Ssc.7176.1.A1_atC—X—C chemokine receptor 3.74 10.91 8.15 1.68 CXCR4 JM 3100 type 4(CXC-R4) (CXCR-4) Ssc.15801.1.A1_at Protein kinase C, beta 3.36 6.363.53 −4.98 PRKCB1 enzastaurin, ruboxistaurin Ssc.12791.1.A1_at3-hydroxy-3-methylglutaryl- 3.27 2.77 1.77 −2.56 HMGCRaspirin/pravastatin, coenzyme A reductase lovastatin/niacin,ezetimibe/simvastatin, amlodipine/atorvastatin, fluvastatin,cerivastatin, atorvastatin, pravastatin, simvastatin, lovastatin,rosuvastatin Ssc.11147.1.S1_at Aldehyde dehydrogenase, 3.18 1.13 2.00−1.68 ALDH2 disulfiram, chlorpropamide mitochondrial Ssc.9565.1.S1_atInterferon-gamma receptor 2.92 1.63 1.41 −1.23 IFNGR1 interferongamma-1b alpha chain Ssc.3607.1.S1_at Interferon-alpha/beta receptor2.28 4.65 1.11 −1.56 IFNAR2 interferon beta-1a, beta interferon alfa-2b,interferon alfacon-1, PEG- interferon alfa-2a, interferonalfa-2a/ribavirin, pegintron, interferon beta- 1b, IFNA2ASsc.4756.1.A1_at Adenosine A3 receptor. 2.15 2.10 1.88 −1.81 ADORA3adenosine, dyphylline, aminophylline, clofarabine, theophylline,caffeine Ssc.10142.1.A1_at Dihydropyrimidine 2.06 2.17 1.13 −2.68 DPYDeniluracil dehydrogenase [NADP+] Ssc.15822.1.S1_at Coagulation factor V1.92 3.76 1.89 −1.75 F5 drotrecogin alfa Ssc.14258.1.S1_at Amyloid betaA4 protein 1.87 3.33 1.34 −1.02 APP AAB-001 precursor (APP) (ABPP)Ssc.15878.1.S1_at Serine/threonine protein 1.85 3.22 3.62 −1.49 PPP3CAISAtx-247, tacrolimus, phosphatase 2B catalytic pimecrolimus,cyclosporin A subunit, alpha Ssc.9272.1.S1_at Tumor-associated calcium1.81 3.94 176.50 2.07 TACSTD1 tucotuzumab celmoleukin signal transducer1 (EPCAM antigen) Ssc.19691.1.S1_at Platelet-activating factor 1.59 1.163.01 1.47 PLA2G7 darapladib acetylhydrolase Ssc.30147.1.A1_at Fibroblastgrowth factor 1.56 1.13 −1.05 −1.18 FGFR2 palifermin receptor 2Ssc.16823.1.S1_at P2Y purinoceptor 12 (P2Y12) 1.38 1.19 1.41 1.11 P2RY12prasugrel, AZD 6140, (P2Y12 platelet ADP receptor) clopidogrelSsc.15999.1.A1_at Vascular endothelial growth 1.24 1.24 18.52 −11.02 KDRAEE 788, sunitinib, AZD factor receptor 2 2171, pazopanib, XL647, CEP7055, BMS-582664, KRN-951, vatalanib, sorafenib, vandetanib, pegaptanibSsc.17224.1.S1_at Toll-like receptor 8 1.17 6.49 3.13 −1.52 TLR6resiquimod Ssc.7297.1.S1_at Amine oxidase 1.16 6.42 7.02 −1.13 MAOBsafinamide, ladostigil, rasagiline, selegiline, dextroamphetamine,procainamide, tranylcypromine, phenelzine, isocarboxazid, benzphetamineSsc.28329.1.S1_at DNA polymerase beta 1.14 1.19 1.07 5.25 POLBnelarabine, clofarabine, stavudine, trifluridine, vidarabine,zalcitabine, entecavir Ssc.19700.1.S1_at Serine/threonine protein 1.111.13 1.34 1.09 PPP3CB ISAtx-247, tacrolimus, phosphatase 2B catalyticpimecrolimus, cyclosporin A subunit, beta Ssc.8726.1.A1_atAmidophosphoribosyltransferase 1.03 1.24 4.16 −1.11 PPAT6-mercaptopurine, precursor thioguanine, azathioprine

TABLE 11 Animal number, days after post-shunt PAH creation surgery, andpulmonary arterial pressure (PAP). Animal Day PAP PAP mean Pig 19Timecourse P19 Day 0 28/1  26 P19 Day 10 22/17 19 P19 Day 24 76/29 47P19 Day 59 89/50 58 P19 Day 94 70/18 54 Pig 20 Timecourse P20 Day 020/11 16 P20 Day 6 19/15 16 P20 Day 21 20/15 17 P20 Day 55 23/15 19 P20Day 83 62/17 45 P20 Day 104 116/72  104 P20 Day 140 92/40 81 Normal(Normal Pressure & Flow) P19 Day 0 28/1  26 P20 Day 0 20/11 16 HFLP(High Flow Low Pressure) P19 Day 10 22/17 19 P20 Day 6 19/15 16 P20 Day21 20/15 17 P20 Day 55 23/15 19 HFHP (High Flow High Pressure) P19 Day24 76/29 47 P19 Day 59 89/50 58 P19 Day 94 70/18 54 P20 Day 83 62/17 45P20 Day 104 116/72  104 P20 Day 140 92/40 81

TABLE 12 Significantly differently expressed downregulated microRNAsHFHP (High Flow High Pressure) vs. normal. Downregulated microRNA HFHPvs. Norm (p < .05) Illumina ID Normal HFHP HFLP miRNA SymbolILMN_3167128 32.58 −2.36 2.75 solexa-603- 1846 ILMN_3167515 4183.7442.62 142.81 hsa-miR-586 ILMN_3168604 31.83 −2.01 0.90 hsa-miR-1201ILMN_3167691 127.02 1.76 1358.98 hsa-miR-33a ILMN_3167249 229.25 18.22511.84 HS_56 ILMN_3167753 114.97 14.32 66.23 hsa-miR- 520d:9.1ILMN_3168215 37.30 8.98 3110.35 hsa-miR-521 ILMN_3168168 32.58 1.7228.59 hsa-miR-519a ILMN_3168054 3916.21 79.38 14.02 HS_134 ILMN_316823558.82 6.34 2.94 HS_169 ILMN_3168335 15.54 −2.85 26.65 HS_221ILMN_3167393 90.38 5.18 5.54 hsa-miR-496 ILMN_3168678 837.14 14.23777.94 hsa-miR-935 ILMN_3167175 8796.46 1274.47 88.95 hsa-miR-542-5pILMN_3168905 92.30 5.07 33.55 solexa-5620- 151 ILMN_3168648 593.72 46.29812.05 hsa-miR-99a ILMN_3167761 37.30 16.59 0.17 hsa-miR-212ILMN_3168709 1281.24 218.10 80.10 hsa-let-7f-2 ILMN_3168446 8875.62343.70 546.81 hsa-miR-494 ILMN_3168663 31.00 3.29 18.23 hsa-miR-1321ILMN_3168597 99.25 14.28 43.96 hsa-miR-219-2- 3p ILMN_3166971 1310.30311.18 924.85 hsa-miR-95 ILMN_3167491 3060.68 925.46 1647.50 hsa-miR-128b:9.1 ILMN_3168654 740.78 96.90 957.01 hsa-miR-33a ILMN_3167052370.00 45.81 234.11 hsa-miR-495 ILMN_3167337 177.30 43.83 27.93hsa-miR-1229 ILMN_3168827 569.48 117.37 51.85 hsa-miR-1205 ILMN_31673286444.52 2162.76 2119.65 hsa-miR-524-3p ILMN_3167952 8724.37 2076.18926.06 HS_150 ILMN_3168798 376.77 151.44 1348.57 hsa-miR-135aILMN_3168558 211.48 68.62 28.31 hsa-miR-483-5p ILMN_3168039 9629.833219.90 7248.74 hsa-miR- 124a:9.1 ILMN_3168755 233.36 82.45 332.03hsa-miR-29b-1 ILMN_3168540 493.90 161.33 304.45 hsa-miR-548c- 5pILMN_3168265 11306.19 5572.32 6108.39 hsa-miR-551a ILMN_3168481 8687.784563.60 5504.04 hsa-miR-377 ILMN_3168882 12023.57 6677.06 8627.69hsa-miR-1304

TABLE 13 Significantly differently expressed upregulated microRNAs HFHP(High Flow High Pressure) vs. normal. Upregulated microRNA HFHP vs. Norm(p < .05) Illumina ID Normal HFHP HFLP miRNA Symbol ILMN_3168350 −6.402772.39 12.69 hsa-miR-520g ILMN_3168706 −3.62 1700.55 8.11hsa-miR-331-5p ILMN_3167244 −4.11 1534.57 −4.19 hsa-miR-410 ILMN_3168710−3.08 1499.40 2147.63 hsa-let-7d ILMN_3168167 −4.14 1144.02 558.78hsa-miR-187 ILMN_3168672 −4.20 941.07 162.41 hsa-miR-16-2 ILMN_3168870−8.25 912.52 8.99 hsa-miR-130a ILMN_3168639 −4.96 728.32 −3.51hsa-miR-548n ILMN_3168719 −1.17 380.69 −2.12 hsa-miR-127-5p ILMN_3168890−4.11 343.04 530.05 solexa-2580- 353 ILMN_3168217 −5.60 304.34 −1.25HS_206 ILMN_3167088 −5.06 303.57 −0.34 hsa-miR-663 ILMN_3168911 −1.32235.62 61.24 solexa-7534- 111 ILMN_3168732 −0.63 216.74 12.96 hsa-let-7gILMN_3167993 −6.45 192.76 237.96 HS_157 ILMN_3167193 −7.25 151.362130.07 hsa-miR-610 ILMN_3167879 −4.09 111.71 11.99 HS_251.1ILMN_3168031 −4.54 52.02 15.76 hsa-miR-519e ILMN_3168818 −4.09 20.75−0.83 hsa-miR-1237 ILMN_3168241 −2.10 18.57 649.52 hsa-miR-1185ILMN_3167470 −4.18 12.39 7.90 HS_151.1 ILMN_3167512 −1.69 11.79 9.99HS_135 ILMN_3168895 −2.86 7.81 0.75 solexa-3126- 285 ILMN_3167158 −0.633.36 739.08 hsa-miR-30a ILMN_3168722 1.26 529.41 430.69 hsa-miR-192ILMN_3167039 17.25 1036.96 883.92 hsa-miR-568 ILMN_3168680 2.62 148.5954.43 hsa-miR-1203 ILMN_3167223 381.67 5756.85 4105.59 hsa-miR-28-5pILMN_3167361 21.39 259.94 255.04 HS_262.1 ILMN_3167684 11.78 80.14 21.38HS_170 ILMN_3168760 11.78 80.09 26.17 hsa-miR-1273 ILMN_3167275 39.19146.84 1900.87 hsa-miR-602 ILMN_3168240 1613.60 5725.95 4943.62hsa-miR-374a ILMN_3168589 597.66 1739.42 928.77 hsa-miR-29a

TABLE 14 Significantly differently expressed downregulated microRNAsHFLP (High Flow Low Pressure) vs. normal. Downregulated microRNA HFLPvs. Norm (p < .05) Illumina ID Normal HFLP HFHP Gene Symbol ILMN_316720927.46 −3.19 1350.01 HS_104 ILMN_3168537 38.77 −0.76 57.24hsa-miR-548a-5p ILMN_3167655 351.30 0.20 74.35 hsa-miR-556-5pILMN_3168235 58.82 2.94 6.34 HS_169 ILMN_3167800 13.08 −2.83 1036.31HS_140 ILMN_3167175 8796.46 88.95 1274.47 hsa-miR-542-5p ILMN_31680543916.21 14.02 79.38 HS_134 ILMN_3167761 37.30 0.17 16.59 hsa-miR-212ILMN_3167509 17.25 −1.53 17.72 hsa-miR-363 ILMN_3167707 130.17 1.4942.39 HS_59 ILMN_3167515 4183.74 142.81 42.62 hsa-miR-586 ILMN_31684468875.62 546.81 343.70 hsa-miR-494 ILMN_3168827 569.48 51.85 117.37hsa-miR-1205 ILMN_3168709 1281.24 80.10 218.10 hsa-let-7f-2 ILMN_3168558211.48 28.31 68.62 hsa-miR-483-5p ILMN_3167952 8724.37 926.06 2076.18HS_150 ILMN_3167337 177.30 27.93 43.83 hsa-miR-1229 ILMN_3168305 31.005.36 34.52 HS_156 ILMN_3168490 67.94 18.69 106.29 hsa-miR-619ILMN_3168573 776.09 190.47 805.44 hsa-miR-10b ILMN_3168586 887.48 304.35617.25 hsa-miR-371-5p

TABLE 15 Significantly differently expressed upregulated microRNAs HFLP(High Flow Low Pressure) vs. normal. Upregulated microRNA HFLP vs. Norm(p < .05) Illumina ID Normal HFLP HFHP miRNA Symbol ILMN_3168010 −9.812363.55 689.66 HS_70 ILMN_3168710 −3.08 2147.63 1499.40 hsa-let-7dILMN_3168167 −4.14 558.78 1144.02 hsa-miR-187 ILMN_3168890 −4.11 530.05343.04 solexa-2580-353 ILMN_3167993 −6.45 237.96 192.76 HS_157ILMN_3168911 −1.32 61.24 235.62 solexa-7534-111 ILMN_3168870 −8.25 8.99912.52 hsa-miR-130a ILMN_3167512 −1.69 9.99 11.79 HS_135 ILMN_31687221.26 430.69 529.41 hsa-miR-192 ILMN_3167720 2.62 145.01 147.62hsa-miR-154 ILMN_3167062 78.98 2184.01 1423.21 hsa-miR-151:9.1ILMN_3168680 2.62 54.43 148.59 hsa-miR-1203 ILMN_3167778 24.39 206.0681.33 hsa-miR-525-3p ILMN_3167749 37.30 226.26 272.25 HS_199

TABLE 16 Significantly differently expressed upregulated microRNAs HFHPvs. HFLP. Upregulated microRNA HFHP vs. HFLP (p < .05) Illumina IDNormal HFHP HFLP miRNA Symbol ILMN_3167244 −4.11 1534.57 −4.19has-miR-410 ILMN_3168639 −4.96 728.32 −3.51 has-miR-548n ILMN_316853738.77 57.24 −0.76 has-miR-548a-5p ILMN_3168613 4.53 18.13 −0.99has-miR-185 ILMN_3168047 34.59 10.25 −4.94 HS_3 ILMN_3167440 71.49 −0.51−4.89 HS_67 ILMN_3168585 45.00 97.09 2.43 has-miR-1250 ILMN_3168543140.56 2778.92 47.17 has-miR-5481 ILMN_3168221 52.52 216.12 13.76has-miR-548c-3p ILMN_3167831 31.83 186.98 12.94 has-miR-520d-5pILMN_3167105 292.19 174.71 25.34 has-miR-208b ILMN_3167313 475.92 793.85135.08 HS_200 ILMN_3168634 892.54 1830.74 479.17 has-miR-218-1ILMN_3168247 390.00 300.41 111.54 has-miR-643

TABLE 17 Significantly differently expressed downregulated microRNAsHFHP vs. HFLP. Downregulated microRNA HFHP vs. HFLP (p < .05) IlluminaID Normal HFHP HFLP miRNA Symbol ILMN_3167778 24.39 81.33 206.06hsa-miR-525-3p ILMN_3167052 370.00 45.81 234.11 hsa-miR-495 ILMN_3168052176.33 116.43 480.71 HS_250 ILMN_3168863 9.59 1.11 46.30 hsa-miR-933ILMN_3168848 13.53 8.90 475.98 hsa-miR-1287 ILMN_3168750 784.33 2850.158118.48 hsa-miR-1308 ILMN_3168348 10.81 9.66 553.87 hsa-miR-133bILMN_3166995 1.97 1.33 254.82 HS_215 ILMN_3167545 42.85 10.92 23.89HS_115 ILMN_3168819 756.53 1345.27 5334.48 hsa-miR-151-5p ILMN_3167249229.25 18.22 511.84 HS_56 ILMN_3168010 −9.81 689.66 2363.55 HS_70ILMN_3168215 37.30 8.98 3110.35 hsa-miR-521

I claim:
 1. A method of treating an individual suffering from the vascular-related disease pulmonary arterial hypertension comprising the steps of: a) obtaining a biopsy sample from the individual's pulmonary artery; b) analyzing gene expression levels of the biopsy sample from the pulmonary artery of the individual and the non-diseased control, wherein the analyzing of gene expression levels are for genes unassociated with the vascular-related disease, and further wherein the gene for which expression is analyzed is chosen from the group consisting of HSPE, YES1, CFTR, MAOA, MAOB, and CACNA2D1; c) comparing the gene expression levels between the biopsy sample from the pulmonary artery of the individual and the non-diseased control; d) identifying at least one gene from step c) that is upregulated or downregulated in the biopsy sample based on the non-diseased control; e) obtaining gene products from the genes identified in step c); and f) selecting pharmaceutical agents which are known inhibitors of the gene products from the at least one upregulated gene or known promoters of the gene products from the at least one downregulated gene, wherein the pharmaceutical agents selected are administered to the individual suffering from the vascular-related disease.
 2. The method of claim 1, wherein the biopsy sample is extracted using an endoarterial catheter.
 3. The method of claim 1, wherein the gene expression levels are analyzed by extracting RNA from the biopsy sample.
 4. The method of claim 3, wherein the RNA is converted to cDNA and the cDNA is compared in step c).
 5. The method of claim 1, wherein step b) is accomplished using a microarray.
 6. The method of claim 1, wherein the individual suffering from the vascular-related disease is in the early stage progression of the vascular-related disease.
 7. The method of claim 6, wherein the pharmaceutical agents to treat the early stage progression of the vascular-related disease is at least one member selected from the group consisting of the drugs listed in Table
 3. 8. The method of claim 1, wherein the individual suffering from the vascular-related disease is in the mid stage progression of the vascular-related disease.
 9. The method of claim 1, wherein the individual suffering from the vascular-related disease is in the late stage progression of the vascular-related disease.
 10. The method of claim 8, wherein the pharmaceutical agents to treat the mid stage progression of the vascular-related disease is at least one member selected from the group consisting of the drugs listed in Tables 4 and
 5. 11. The method of claim 9, wherein the pharmaceutical agents to treat the late stage progression of the vascular-related disease is at least one member selected from the group consisting of the drugs listed in Table
 6. 